[2024-01-24 13:57:31,987] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,993] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,993] [INFO] DQC Reference Directory: /var/lib/cwl/stg2331874d-fc7e-4558-b476-2b682ac849e6/dqc_reference
[2024-01-24 13:57:33,383] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,384] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,385] [INFO] Running command: gunzip -c /var/lib/cwl/stgb287a64a-ab52-4c3e-ac0a-136641e8567e/GCF_024978135.1_ASM2497813v1_genomic.fna.gz | prodigal -d GCF_024978135.1_ASM2497813v1_genomic.fna/cds.fna -a GCF_024978135.1_ASM2497813v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:43,909] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:43,909] [INFO] Task started: HMMsearch
[2024-01-24 13:57:43,909] [INFO] Running command: hmmsearch --tblout GCF_024978135.1_ASM2497813v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2331874d-fc7e-4558-b476-2b682ac849e6/dqc_reference/reference_markers.hmm GCF_024978135.1_ASM2497813v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:44,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:44,231] [INFO] Found 6/6 markers.
[2024-01-24 13:57:44,271] [INFO] Query marker FASTA was written to GCF_024978135.1_ASM2497813v1_genomic.fna/markers.fasta
[2024-01-24 13:57:44,271] [INFO] Task started: Blastn
[2024-01-24 13:57:44,271] [INFO] Running command: blastn -query GCF_024978135.1_ASM2497813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2331874d-fc7e-4558-b476-2b682ac849e6/dqc_reference/reference_markers.fasta -out GCF_024978135.1_ASM2497813v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:45,531] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:45,534] [INFO] Selected 11 target genomes.
[2024-01-24 13:57:45,535] [INFO] Target genome list was writen to GCF_024978135.1_ASM2497813v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:45,539] [INFO] Task started: fastANI
[2024-01-24 13:57:45,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgb287a64a-ab52-4c3e-ac0a-136641e8567e/GCF_024978135.1_ASM2497813v1_genomic.fna.gz --refList GCF_024978135.1_ASM2497813v1_genomic.fna/target_genomes.txt --output GCF_024978135.1_ASM2497813v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:56,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:56,066] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2331874d-fc7e-4558-b476-2b682ac849e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:56,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2331874d-fc7e-4558-b476-2b682ac849e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:56,076] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:57:56,076] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:57:56,077] [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	90.7317	1070	1275	95	below_threshold
Herbiconiux solani	strain=NBRC 106740	GCA_001571005.1	661329	661329	type	True	83.9623	792	1275	95	below_threshold
Herbiconiux moechotypicola	strain=KCTC 19653	GCA_024979255.1	637393	637393	type	True	83.2001	766	1275	95	below_threshold
Herbiconiux ginsengi	strain=CGMCC 4.3491	GCA_900107435.1	381665	381665	type	True	83.019	766	1275	95	below_threshold
Cnuibacter physcomitrellae	strain=CGMCC 1.15041	GCA_014640535.1	1619308	1619308	type	True	81.1364	681	1275	95	below_threshold
Cnuibacter physcomitrellae	strain=XA(T)	GCA_002096055.1	1619308	1619308	type	True	81.0308	707	1275	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	79.5431	532	1275	95	below_threshold
Clavibacter zhangzhiyongii	strain=DM1	GCA_014775655.1	2768071	2768071	type	True	79.3711	474	1275	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_021922985.1	31965	28447	type	True	79.2515	495	1275	95	below_threshold
Clavibacter michiganensis subsp. tessellarius	strain=ATCC 33566	GCA_002240635.1	31965	28447	type	True	79.2222	489	1275	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	79.1397	486	1275	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:56,079] [INFO] DFAST Taxonomy check result was written to GCF_024978135.1_ASM2497813v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:56,080] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:56,080] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:56,080] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2331874d-fc7e-4558-b476-2b682ac849e6/dqc_reference/checkm_data
[2024-01-24 13:57:56,081] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:56,120] [INFO] Task started: CheckM
[2024-01-24 13:57:56,121] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024978135.1_ASM2497813v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024978135.1_ASM2497813v1_genomic.fna/checkm_input GCF_024978135.1_ASM2497813v1_genomic.fna/checkm_result
[2024-01-24 13:58:48,674] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:48,675] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:48,719] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:48,719] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:48,720] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024978135.1_ASM2497813v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:48,720] [INFO] Task started: Blastn
[2024-01-24 13:58:48,720] [INFO] Running command: blastn -query GCF_024978135.1_ASM2497813v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2331874d-fc7e-4558-b476-2b682ac849e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_024978135.1_ASM2497813v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:50,856] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:50,859] [INFO] Selected 7 target genomes.
[2024-01-24 13:58:50,860] [INFO] Target genome list was writen to GCF_024978135.1_ASM2497813v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:50,871] [INFO] Task started: fastANI
[2024-01-24 13:58:50,871] [INFO] Running command: fastANI --query /var/lib/cwl/stgb287a64a-ab52-4c3e-ac0a-136641e8567e/GCF_024978135.1_ASM2497813v1_genomic.fna.gz --refList GCF_024978135.1_ASM2497813v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024978135.1_ASM2497813v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:59,177] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:59,185] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:58:59,185] [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_015350805.1	s__Herbiconiux sp015350805	91.0234	1070	1275	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	90.7469	1069	1275	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	83.9636	792	1275	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	83.4004	831	1275	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	83.3994	770	1275	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	83.0186	766	1275	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	82.9289	732	1275	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 13:58:59,187] [INFO] GTDB search result was written to GCF_024978135.1_ASM2497813v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:59,187] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:59,190] [INFO] DFAST_QC result json was written to GCF_024978135.1_ASM2497813v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:59,191] [INFO] DFAST_QC completed!
[2024-01-24 13:58:59,191] [INFO] Total running time: 0h1m27s