[2024-01-24 14:54:50,513] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:50,516] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:50,516] [INFO] DQC Reference Directory: /var/lib/cwl/stgb687fd97-9518-4753-93c2-c8a89af23c7e/dqc_reference
[2024-01-24 14:54:51,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:51,808] [INFO] Task started: Prodigal
[2024-01-24 14:54:51,808] [INFO] Running command: gunzip -c /var/lib/cwl/stg96624491-fe11-408a-9441-172a83157285/GCF_004216665.1_ASM421666v1_genomic.fna.gz | prodigal -d GCF_004216665.1_ASM421666v1_genomic.fna/cds.fna -a GCF_004216665.1_ASM421666v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:03,204] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:03,205] [INFO] Task started: HMMsearch
[2024-01-24 14:55:03,205] [INFO] Running command: hmmsearch --tblout GCF_004216665.1_ASM421666v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb687fd97-9518-4753-93c2-c8a89af23c7e/dqc_reference/reference_markers.hmm GCF_004216665.1_ASM421666v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:03,520] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:03,521] [INFO] Found 6/6 markers.
[2024-01-24 14:55:03,558] [INFO] Query marker FASTA was written to GCF_004216665.1_ASM421666v1_genomic.fna/markers.fasta
[2024-01-24 14:55:03,558] [INFO] Task started: Blastn
[2024-01-24 14:55:03,558] [INFO] Running command: blastn -query GCF_004216665.1_ASM421666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb687fd97-9518-4753-93c2-c8a89af23c7e/dqc_reference/reference_markers.fasta -out GCF_004216665.1_ASM421666v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:04,912] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:04,916] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:04,917] [INFO] Target genome list was writen to GCF_004216665.1_ASM421666v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:04,937] [INFO] Task started: fastANI
[2024-01-24 14:55:04,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg96624491-fe11-408a-9441-172a83157285/GCF_004216665.1_ASM421666v1_genomic.fna.gz --refList GCF_004216665.1_ASM421666v1_genomic.fna/target_genomes.txt --output GCF_004216665.1_ASM421666v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:17,495] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:17,495] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb687fd97-9518-4753-93c2-c8a89af23c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:17,496] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb687fd97-9518-4753-93c2-c8a89af23c7e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:17,507] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:55:17,507] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:55:17,507] [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
Agromyces ramosus	strain=DSM 43045	GCA_004216665.1	33879	33879	type	True	100.0	1276	1276	95	conclusive
Agromyces humi	strain=ANK073	GCA_009720255.2	1766800	1766800	type	True	86.2715	669	1276	95	below_threshold
Agromyces mariniharenae	strain=NEAU-184	GCA_008122505.1	2604423	2604423	type	True	86.0294	1003	1276	95	below_threshold
Agromyces bauzanensis	strain=CGMCC 1.8984	GCA_014645655.1	1308924	1308924	type	True	84.3143	770	1276	95	below_threshold
Agromyces tardus	strain=SJ-23	GCA_003710805.1	2583849	2583849	type	True	83.9174	872	1276	95	below_threshold
Agromyces badenianii	strain=MF30-A	GCA_003070885.1	2080742	2080742	type	True	83.6006	765	1276	95	below_threshold
Agromyces albus	strain=DSM 15934	GCA_004134825.1	205332	205332	type	True	83.5984	825	1276	95	below_threshold
Agromyces cavernae	strain=SYSU K20354	GCA_021044935.1	2898659	2898659	type	True	83.4473	844	1276	95	below_threshold
Agromyces humatus	strain=JCM 14319	GCA_021228295.1	279573	279573	type	True	83.241	854	1276	95	below_threshold
Agromyces allii	strain=JCM 13584	GCA_009749385.1	393607	393607	type	True	83.2051	846	1276	95	below_threshold
Agromyces binzhouensis	strain=CGMCC 4.7180	GCA_004135055.1	1817495	1817495	type	True	83.017	553	1276	95	below_threshold
Agromyces agglutinans	strain=CFH 90414	GCA_009647605.1	2662258	2662258	type	True	82.5612	796	1276	95	below_threshold
Agromyces archimandritae	strain=G127AT	GCA_018024495.1	2781962	2781962	type	True	80.8074	612	1276	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:17,509] [INFO] DFAST Taxonomy check result was written to GCF_004216665.1_ASM421666v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:17,509] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:17,510] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:17,510] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb687fd97-9518-4753-93c2-c8a89af23c7e/dqc_reference/checkm_data
[2024-01-24 14:55:17,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:17,549] [INFO] Task started: CheckM
[2024-01-24 14:55:17,549] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216665.1_ASM421666v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216665.1_ASM421666v1_genomic.fna/checkm_input GCF_004216665.1_ASM421666v1_genomic.fna/checkm_result
[2024-01-24 14:56:18,838] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:18,840] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:18,864] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:18,865] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:18,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216665.1_ASM421666v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:18,866] [INFO] Task started: Blastn
[2024-01-24 14:56:18,866] [INFO] Running command: blastn -query GCF_004216665.1_ASM421666v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb687fd97-9518-4753-93c2-c8a89af23c7e/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216665.1_ASM421666v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:21,100] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:21,104] [INFO] Selected 10 target genomes.
[2024-01-24 14:56:21,104] [INFO] Target genome list was writen to GCF_004216665.1_ASM421666v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:21,118] [INFO] Task started: fastANI
[2024-01-24 14:56:21,119] [INFO] Running command: fastANI --query /var/lib/cwl/stg96624491-fe11-408a-9441-172a83157285/GCF_004216665.1_ASM421666v1_genomic.fna.gz --refList GCF_004216665.1_ASM421666v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216665.1_ASM421666v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:31,665] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:31,680] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:31,680] [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_004216665.1	s__Agromyces ramosus	100.0	1276	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009720255.1	s__Agromyces humi	86.2716	669	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001428255.1	s__Agromyces sp001428255	86.1648	985	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122505.1	s__Agromyces sp008122505	86.0035	1006	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715355.1	s__Agromyces sp006715355	84.6657	920	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645655.1	s__Agromyces bauzanensis	84.3146	770	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004959775.1	s__Agromyces sp004959775	84.1837	874	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003070885.1	s__Agromyces badenianii	83.6082	765	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	98.76	98.76	0.96	0.96	2	-
GCF_001429165.1	s__Agromyces sp001429165	83.4738	797	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003384855.1	s__Agromyces sp003384855	83.3262	840	1276	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:31,682] [INFO] GTDB search result was written to GCF_004216665.1_ASM421666v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:31,682] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:31,685] [INFO] DFAST_QC result json was written to GCF_004216665.1_ASM421666v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:31,686] [INFO] DFAST_QC completed!
[2024-01-24 14:56:31,686] [INFO] Total running time: 0h1m41s