[2024-01-24 14:22:16,228] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:16,230] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:16,230] [INFO] DQC Reference Directory: /var/lib/cwl/stge6fe6b58-3b7d-4218-a11e-fdea80040f1b/dqc_reference
[2024-01-24 14:22:17,463] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:17,464] [INFO] Task started: Prodigal
[2024-01-24 14:22:17,464] [INFO] Running command: gunzip -c /var/lib/cwl/stga5d0dd3b-3268-4501-9a90-1a08c5f03acc/GCF_013409865.1_ASM1340986v1_genomic.fna.gz | prodigal -d GCF_013409865.1_ASM1340986v1_genomic.fna/cds.fna -a GCF_013409865.1_ASM1340986v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:28,071] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:28,072] [INFO] Task started: HMMsearch
[2024-01-24 14:22:28,072] [INFO] Running command: hmmsearch --tblout GCF_013409865.1_ASM1340986v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge6fe6b58-3b7d-4218-a11e-fdea80040f1b/dqc_reference/reference_markers.hmm GCF_013409865.1_ASM1340986v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:28,366] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:28,368] [INFO] Found 6/6 markers.
[2024-01-24 14:22:28,414] [INFO] Query marker FASTA was written to GCF_013409865.1_ASM1340986v1_genomic.fna/markers.fasta
[2024-01-24 14:22:28,414] [INFO] Task started: Blastn
[2024-01-24 14:22:28,414] [INFO] Running command: blastn -query GCF_013409865.1_ASM1340986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6fe6b58-3b7d-4218-a11e-fdea80040f1b/dqc_reference/reference_markers.fasta -out GCF_013409865.1_ASM1340986v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:29,743] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:29,747] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:29,748] [INFO] Target genome list was writen to GCF_013409865.1_ASM1340986v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:29,762] [INFO] Task started: fastANI
[2024-01-24 14:22:29,762] [INFO] Running command: fastANI --query /var/lib/cwl/stga5d0dd3b-3268-4501-9a90-1a08c5f03acc/GCF_013409865.1_ASM1340986v1_genomic.fna.gz --refList GCF_013409865.1_ASM1340986v1_genomic.fna/target_genomes.txt --output GCF_013409865.1_ASM1340986v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:38,971] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:38,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge6fe6b58-3b7d-4218-a11e-fdea80040f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:38,972] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge6fe6b58-3b7d-4218-a11e-fdea80040f1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:38,985] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:38,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:38,985] [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 flava	strain=DSM 26474	GCA_013409865.1	881268	881268	type	True	100.0	1281	1282	95	conclusive
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	84.0013	813	1282	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	83.1591	763	1282	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	83.0218	786	1282	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	81.2464	694	1282	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	81.1576	709	1282	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.7638	485	1282	95	below_threshold
Clavibacter phaseoli	strain=LPPA 982	GCA_021922925.1	1734031	1734031	type	True	79.7328	485	1282	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.6522	551	1282	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.5784	498	1282	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.4732	499	1282	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:38,987] [INFO] DFAST Taxonomy check result was written to GCF_013409865.1_ASM1340986v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:38,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:38,987] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:38,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge6fe6b58-3b7d-4218-a11e-fdea80040f1b/dqc_reference/checkm_data
[2024-01-24 14:22:38,989] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:39,034] [INFO] Task started: CheckM
[2024-01-24 14:22:39,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013409865.1_ASM1340986v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013409865.1_ASM1340986v1_genomic.fna/checkm_input GCF_013409865.1_ASM1340986v1_genomic.fna/checkm_result
[2024-01-24 14:23:30,193] [INFO] Task succeeded: CheckM
[2024-01-24 14:23:30,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:23:30,219] [INFO] ===== Completeness check finished =====
[2024-01-24 14:23:30,219] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:23:30,220] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013409865.1_ASM1340986v1_genomic.fna/markers.fasta)
[2024-01-24 14:23:30,220] [INFO] Task started: Blastn
[2024-01-24 14:23:30,220] [INFO] Running command: blastn -query GCF_013409865.1_ASM1340986v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge6fe6b58-3b7d-4218-a11e-fdea80040f1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_013409865.1_ASM1340986v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:32,363] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:32,366] [INFO] Selected 7 target genomes.
[2024-01-24 14:23:32,366] [INFO] Target genome list was writen to GCF_013409865.1_ASM1340986v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:23:32,372] [INFO] Task started: fastANI
[2024-01-24 14:23:32,373] [INFO] Running command: fastANI --query /var/lib/cwl/stga5d0dd3b-3268-4501-9a90-1a08c5f03acc/GCF_013409865.1_ASM1340986v1_genomic.fna.gz --refList GCF_013409865.1_ASM1340986v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013409865.1_ASM1340986v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:23:39,638] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:39,651] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:23:39,651] [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_013409865.1	s__Herbiconiux flava	100.0	1281	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	95.35	95.35	0.90	0.90	2	conclusive
GCF_015350805.1	s__Herbiconiux sp015350805	93.1292	1095	1282	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	84.0252	811	1282	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	83.5822	777	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	99.99	99.99	0.97	0.97	2	-
GCF_013113715.1	s__Herbiconiux sp013113715	83.4833	831	1282	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Herbiconiux	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107435.1	s__Herbiconiux ginsengi	83.0473	783	1282	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	83.0351	733	1282	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 14:23:39,653] [INFO] GTDB search result was written to GCF_013409865.1_ASM1340986v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:23:39,654] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:23:39,657] [INFO] DFAST_QC result json was written to GCF_013409865.1_ASM1340986v1_genomic.fna/dqc_result.json
[2024-01-24 14:23:39,657] [INFO] DFAST_QC completed!
[2024-01-24 14:23:39,657] [INFO] Total running time: 0h1m23s