[2024-01-24 12:39:35,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:39:35,649] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:39:35,650] [INFO] DQC Reference Directory: /var/lib/cwl/stg0835e8e3-d200-40a6-bb0b-05851b1e6741/dqc_reference
[2024-01-24 12:39:36,877] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:39:36,878] [INFO] Task started: Prodigal
[2024-01-24 12:39:36,878] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6d2cb97-3b80-461f-9dc6-45acfa0be19d/GCF_024979295.1_ASM2497929v1_genomic.fna.gz | prodigal -d GCF_024979295.1_ASM2497929v1_genomic.fna/cds.fna -a GCF_024979295.1_ASM2497929v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:39:51,272] [INFO] Task succeeded: Prodigal
[2024-01-24 12:39:51,272] [INFO] Task started: HMMsearch
[2024-01-24 12:39:51,272] [INFO] Running command: hmmsearch --tblout GCF_024979295.1_ASM2497929v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0835e8e3-d200-40a6-bb0b-05851b1e6741/dqc_reference/reference_markers.hmm GCF_024979295.1_ASM2497929v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:39:51,564] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:39:51,565] [INFO] Found 6/6 markers.
[2024-01-24 12:39:51,616] [INFO] Query marker FASTA was written to GCF_024979295.1_ASM2497929v1_genomic.fna/markers.fasta
[2024-01-24 12:39:51,616] [INFO] Task started: Blastn
[2024-01-24 12:39:51,616] [INFO] Running command: blastn -query GCF_024979295.1_ASM2497929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0835e8e3-d200-40a6-bb0b-05851b1e6741/dqc_reference/reference_markers.fasta -out GCF_024979295.1_ASM2497929v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:39:52,854] [INFO] Task succeeded: Blastn
[2024-01-24 12:39:52,858] [INFO] Selected 15 target genomes.
[2024-01-24 12:39:52,858] [INFO] Target genome list was writen to GCF_024979295.1_ASM2497929v1_genomic.fna/target_genomes.txt
[2024-01-24 12:39:52,863] [INFO] Task started: fastANI
[2024-01-24 12:39:52,863] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d2cb97-3b80-461f-9dc6-45acfa0be19d/GCF_024979295.1_ASM2497929v1_genomic.fna.gz --refList GCF_024979295.1_ASM2497929v1_genomic.fna/target_genomes.txt --output GCF_024979295.1_ASM2497929v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:40:04,259] [INFO] Task succeeded: fastANI
[2024-01-24 12:40:04,260] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0835e8e3-d200-40a6-bb0b-05851b1e6741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:40:04,260] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0835e8e3-d200-40a6-bb0b-05851b1e6741/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:40:04,273] [INFO] Found 15 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:40:04,273] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:40:04,273] [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
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	83.9449	902	1526	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	83.1984	834	1526	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	83.1039	801	1526	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	82.7202	775	1526	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	80.5146	675	1526	95	below_threshold
Subtercola boreus	strain=K300	GCA_003399685.1	120213	120213	suspected-type	True	79.5121	525	1526	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_003576155.1	1401995	1401995	type	True	79.2587	343	1526	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.2024	544	1526	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.0378	444	1526	95	below_threshold
Agromyces fucosus	strain=CCUG 35506	GCA_004134865.1	41985	41985	type	True	79.0199	512	1526	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.9485	431	1526	95	below_threshold
Clavibacter californiensis	strain=CFBP 8216	GCA_021952865.1	1401995	1401995	type	True	78.9318	423	1526	95	below_threshold
Agromyces flavus	strain=CPCC 202695	GCA_004366335.2	589382	589382	type	True	78.9276	464	1526	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	78.8217	460	1526	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.7942	512	1526	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:40:04,276] [INFO] DFAST Taxonomy check result was written to GCF_024979295.1_ASM2497929v1_genomic.fna/tc_result.tsv
[2024-01-24 12:40:04,276] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:40:04,277] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:40:04,277] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0835e8e3-d200-40a6-bb0b-05851b1e6741/dqc_reference/checkm_data
[2024-01-24 12:40:04,278] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:40:04,332] [INFO] Task started: CheckM
[2024-01-24 12:40:04,332] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024979295.1_ASM2497929v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024979295.1_ASM2497929v1_genomic.fna/checkm_input GCF_024979295.1_ASM2497929v1_genomic.fna/checkm_result
[2024-01-24 12:40:55,109] [INFO] Task succeeded: CheckM
[2024-01-24 12:40:55,110] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:40:55,136] [INFO] ===== Completeness check finished =====
[2024-01-24 12:40:55,136] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:40:55,137] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024979295.1_ASM2497929v1_genomic.fna/markers.fasta)
[2024-01-24 12:40:55,137] [INFO] Task started: Blastn
[2024-01-24 12:40:55,138] [INFO] Running command: blastn -query GCF_024979295.1_ASM2497929v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0835e8e3-d200-40a6-bb0b-05851b1e6741/dqc_reference/reference_markers_gtdb.fasta -out GCF_024979295.1_ASM2497929v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:40:57,167] [INFO] Task succeeded: Blastn
[2024-01-24 12:40:57,171] [INFO] Selected 9 target genomes.
[2024-01-24 12:40:57,171] [INFO] Target genome list was writen to GCF_024979295.1_ASM2497929v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:40:57,177] [INFO] Task started: fastANI
[2024-01-24 12:40:57,177] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6d2cb97-3b80-461f-9dc6-45acfa0be19d/GCF_024979295.1_ASM2497929v1_genomic.fna.gz --refList GCF_024979295.1_ASM2497929v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024979295.1_ASM2497929v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:41:05,607] [INFO] Task succeeded: fastANI
[2024-01-24 12:41:05,620] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:41:05,620] [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
GCA_005502775.1	s__Herbiconiux sp005502775	84.0435	841	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	99.99	99.99	0.97	0.97	2	-
GCF_900107435.1	s__Herbiconiux ginsengi	83.9457	903	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015350805.1	s__Herbiconiux sp015350805	83.2613	829	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409865.1	s__Herbiconiux flava	83.2013	834	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCF_001571005.1	s__Herbiconiux solani	83.0821	803	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297105.1	s__Herbiconiux sp004297105	83.0672	746	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013113715.1	s__Herbiconiux sp013113715	82.9056	809	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	78.9138	498	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004402595.1	s__Cryobacterium sp004402595	78.7451	391	1526	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Cryobacterium	95.0	99.65	99.58	0.91	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:41:05,622] [INFO] GTDB search result was written to GCF_024979295.1_ASM2497929v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:41:05,623] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:41:05,626] [INFO] DFAST_QC result json was written to GCF_024979295.1_ASM2497929v1_genomic.fna/dqc_result.json
[2024-01-24 12:41:05,627] [INFO] DFAST_QC completed!
[2024-01-24 12:41:05,627] [INFO] Total running time: 0h1m30s