[2024-01-24 12:36:24,616] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:36:24,620] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:36:24,620] [INFO] DQC Reference Directory: /var/lib/cwl/stg5bce79e4-e627-4fed-99b6-c3512054a208/dqc_reference
[2024-01-24 12:36:26,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:36:26,029] [INFO] Task started: Prodigal
[2024-01-24 12:36:26,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a30623f-325a-4bae-8f47-c3c659cc414e/GCF_024979235.1_ASM2497923v1_genomic.fna.gz | prodigal -d GCF_024979235.1_ASM2497923v1_genomic.fna/cds.fna -a GCF_024979235.1_ASM2497923v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:36:38,719] [INFO] Task succeeded: Prodigal
[2024-01-24 12:36:38,719] [INFO] Task started: HMMsearch
[2024-01-24 12:36:38,719] [INFO] Running command: hmmsearch --tblout GCF_024979235.1_ASM2497923v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5bce79e4-e627-4fed-99b6-c3512054a208/dqc_reference/reference_markers.hmm GCF_024979235.1_ASM2497923v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:36:38,990] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:36:38,991] [INFO] Found 6/6 markers.
[2024-01-24 12:36:39,030] [INFO] Query marker FASTA was written to GCF_024979235.1_ASM2497923v1_genomic.fna/markers.fasta
[2024-01-24 12:36:39,030] [INFO] Task started: Blastn
[2024-01-24 12:36:39,030] [INFO] Running command: blastn -query GCF_024979235.1_ASM2497923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bce79e4-e627-4fed-99b6-c3512054a208/dqc_reference/reference_markers.fasta -out GCF_024979235.1_ASM2497923v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:36:40,188] [INFO] Task succeeded: Blastn
[2024-01-24 12:36:40,191] [INFO] Selected 11 target genomes.
[2024-01-24 12:36:40,191] [INFO] Target genome list was writen to GCF_024979235.1_ASM2497923v1_genomic.fna/target_genomes.txt
[2024-01-24 12:36:40,197] [INFO] Task started: fastANI
[2024-01-24 12:36:40,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a30623f-325a-4bae-8f47-c3c659cc414e/GCF_024979235.1_ASM2497923v1_genomic.fna.gz --refList GCF_024979235.1_ASM2497923v1_genomic.fna/target_genomes.txt --output GCF_024979235.1_ASM2497923v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:36:49,718] [INFO] Task succeeded: fastANI
[2024-01-24 12:36:49,719] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5bce79e4-e627-4fed-99b6-c3512054a208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:36:49,719] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5bce79e4-e627-4fed-99b6-c3512054a208/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:36:49,735] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:36:49,735] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:36:49,735] [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	87.5982	1019	1384	95	below_threshold
Herbiconiux flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	82.7076	767	1384	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	82.6055	770	1384	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	82.1088	727	1384	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	80.0506	609	1384	95	below_threshold
Subtercola boreus	strain=K300	GCA_003399685.1	120213	120213	suspected-type	True	79.4142	474	1384	95	below_threshold
Clavibacter michiganensis subsp. insidiosus	strain=ATCC 10253	GCA_003076355.1	33014	28447	type	True	78.7478	374	1384	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	78.7348	457	1384	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	78.7045	471	1384	95	below_threshold
Clavibacter michiganensis	strain=LMG7333	GCA_021216655.1	28447	28447	suspected-type	True	78.6693	391	1384	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	78.5754	452	1384	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:36:49,737] [INFO] DFAST Taxonomy check result was written to GCF_024979235.1_ASM2497923v1_genomic.fna/tc_result.tsv
[2024-01-24 12:36:49,737] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:36:49,737] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:36:49,738] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5bce79e4-e627-4fed-99b6-c3512054a208/dqc_reference/checkm_data
[2024-01-24 12:36:49,739] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:36:49,778] [INFO] Task started: CheckM
[2024-01-24 12:36:49,778] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024979235.1_ASM2497923v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024979235.1_ASM2497923v1_genomic.fna/checkm_input GCF_024979235.1_ASM2497923v1_genomic.fna/checkm_result
[2024-01-24 12:37:35,149] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:35,150] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:35,169] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:35,169] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:35,170] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024979235.1_ASM2497923v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:35,170] [INFO] Task started: Blastn
[2024-01-24 12:37:35,170] [INFO] Running command: blastn -query GCF_024979235.1_ASM2497923v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5bce79e4-e627-4fed-99b6-c3512054a208/dqc_reference/reference_markers_gtdb.fasta -out GCF_024979235.1_ASM2497923v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:36,984] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:36,988] [INFO] Selected 7 target genomes.
[2024-01-24 12:37:36,989] [INFO] Target genome list was writen to GCF_024979235.1_ASM2497923v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:36,997] [INFO] Task started: fastANI
[2024-01-24 12:37:36,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a30623f-325a-4bae-8f47-c3c659cc414e/GCF_024979235.1_ASM2497923v1_genomic.fna.gz --refList GCF_024979235.1_ASM2497923v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024979235.1_ASM2497923v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:37:43,704] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:43,714] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:37:43,714] [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_900107435.1	s__Herbiconiux ginsengi	87.5982	1019	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCA_005502775.1	s__Herbiconiux sp005502775	83.3337	770	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	99.99	99.99	0.97	0.97	2	-
GCF_015350805.1	s__Herbiconiux sp015350805	82.7274	772	1384	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	82.7264	768	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	-
GCA_004297105.1	s__Herbiconiux sp004297105	82.7146	726	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571005.1	s__Herbiconiux solani	82.5844	772	1384	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	82.4393	757	1384	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:37:43,716] [INFO] GTDB search result was written to GCF_024979235.1_ASM2497923v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:37:43,717] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:37:43,722] [INFO] DFAST_QC result json was written to GCF_024979235.1_ASM2497923v1_genomic.fna/dqc_result.json
[2024-01-24 12:37:43,722] [INFO] DFAST_QC completed!
[2024-01-24 12:37:43,722] [INFO] Total running time: 0h1m19s