[2023-06-18 18:31:20,022] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:20,025] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:20,025] [INFO] DQC Reference Directory: /var/lib/cwl/stgd229bf2c-d717-4e6e-b51c-e6ab38201f34/dqc_reference
[2023-06-18 18:31:21,435] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:21,436] [INFO] Task started: Prodigal
[2023-06-18 18:31:21,436] [INFO] Running command: gunzip -c /var/lib/cwl/stgdad9b447-ad0b-4cb5-b593-a27f90299ae4/GCA_018665855.1_ASM1866585v1_genomic.fna.gz | prodigal -d GCA_018665855.1_ASM1866585v1_genomic.fna/cds.fna -a GCA_018665855.1_ASM1866585v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:37,656] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:37,656] [INFO] Task started: HMMsearch
[2023-06-18 18:31:37,657] [INFO] Running command: hmmsearch --tblout GCA_018665855.1_ASM1866585v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd229bf2c-d717-4e6e-b51c-e6ab38201f34/dqc_reference/reference_markers.hmm GCA_018665855.1_ASM1866585v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:38,033] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:38,034] [INFO] Found 6/6 markers.
[2023-06-18 18:31:38,088] [INFO] Query marker FASTA was written to GCA_018665855.1_ASM1866585v1_genomic.fna/markers.fasta
[2023-06-18 18:31:38,089] [INFO] Task started: Blastn
[2023-06-18 18:31:38,089] [INFO] Running command: blastn -query GCA_018665855.1_ASM1866585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd229bf2c-d717-4e6e-b51c-e6ab38201f34/dqc_reference/reference_markers.fasta -out GCA_018665855.1_ASM1866585v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:38,720] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:38,724] [INFO] Selected 25 target genomes.
[2023-06-18 18:31:38,725] [INFO] Target genome list was writen to GCA_018665855.1_ASM1866585v1_genomic.fna/target_genomes.txt
[2023-06-18 18:31:38,731] [INFO] Task started: fastANI
[2023-06-18 18:31:38,731] [INFO] Running command: fastANI --query /var/lib/cwl/stgdad9b447-ad0b-4cb5-b593-a27f90299ae4/GCA_018665855.1_ASM1866585v1_genomic.fna.gz --refList GCA_018665855.1_ASM1866585v1_genomic.fna/target_genomes.txt --output GCA_018665855.1_ASM1866585v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:57,956] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:57,957] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd229bf2c-d717-4e6e-b51c-e6ab38201f34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:57,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd229bf2c-d717-4e6e-b51c-e6ab38201f34/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:57,968] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 18:31:57,968] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 18:31:57,969] [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 terreus	strain=JCM 14581	GCA_009749465.1	424795	424795	type	True	74.7711	55	1659	95	below_threshold
Deinococcus metalli	strain=DSM 27521	GCA_014201805.1	1141878	1141878	type	True	74.7704	51	1659	95	below_threshold
Cellulosimicrobium arenosum	strain=KCTC 49039	GCA_014837295.1	2708133	2708133	type	True	74.7496	61	1659	95	below_threshold
Agromyces intestinalis	strain=KACC 19306	GCA_008365295.1	2592652	2592652	type	True	74.7336	54	1659	95	below_threshold
Rubrivivax benzoatilyticus	strain=JA2	GCA_000190375.2	316997	316997	type	True	74.7271	62	1659	95	below_threshold
Saccharothrix carnea	strain=CGMCC 4.7097	GCA_003014735.1	1280637	1280637	type	True	74.6898	74	1659	95	below_threshold
Agromyces protaetiae	strain=FW100M-8	GCA_004135405.1	2509455	2509455	type	True	74.6794	72	1659	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 18:31:57,971] [INFO] DFAST Taxonomy check result was written to GCA_018665855.1_ASM1866585v1_genomic.fna/tc_result.tsv
[2023-06-18 18:31:57,971] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:57,971] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:57,972] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd229bf2c-d717-4e6e-b51c-e6ab38201f34/dqc_reference/checkm_data
[2023-06-18 18:31:57,973] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:58,032] [INFO] Task started: CheckM
[2023-06-18 18:31:58,032] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018665855.1_ASM1866585v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018665855.1_ASM1866585v1_genomic.fna/checkm_input GCA_018665855.1_ASM1866585v1_genomic.fna/checkm_result
[2023-06-18 18:32:44,587] [INFO] Task succeeded: CheckM
[2023-06-18 18:32:44,589] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:32:44,610] [INFO] ===== Completeness check finished =====
[2023-06-18 18:32:44,610] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:32:44,610] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018665855.1_ASM1866585v1_genomic.fna/markers.fasta)
[2023-06-18 18:32:44,611] [INFO] Task started: Blastn
[2023-06-18 18:32:44,611] [INFO] Running command: blastn -query GCA_018665855.1_ASM1866585v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd229bf2c-d717-4e6e-b51c-e6ab38201f34/dqc_reference/reference_markers_gtdb.fasta -out GCA_018665855.1_ASM1866585v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:32:45,469] [INFO] Task succeeded: Blastn
[2023-06-18 18:32:45,474] [INFO] Selected 19 target genomes.
[2023-06-18 18:32:45,474] [INFO] Target genome list was writen to GCA_018665855.1_ASM1866585v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:32:45,488] [INFO] Task started: fastANI
[2023-06-18 18:32:45,488] [INFO] Running command: fastANI --query /var/lib/cwl/stgdad9b447-ad0b-4cb5-b593-a27f90299ae4/GCA_018665855.1_ASM1866585v1_genomic.fna.gz --refList GCA_018665855.1_ASM1866585v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018665855.1_ASM1866585v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:32:58,383] [INFO] Task succeeded: fastANI
[2023-06-18 18:32:58,396] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 18:32:58,396] [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_018644665.1	s__GCA-2687025 sp018644665	99.905	1627	1659	d__Bacteria;p__Poribacteria;c__WGA-4E;o__GCA-2687025;f__GCA-2687025;g__GCA-2687025	95.0	99.94	99.91	0.97	0.97	3	conclusive
GCA_002687025.1	s__GCA-2687025 sp002687025	83.8829	956	1659	d__Bacteria;p__Poribacteria;c__WGA-4E;o__GCA-2687025;f__GCA-2687025;g__GCA-2687025	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016866785.1	s__VGLH01 sp016866785	76.2294	155	1659	d__Bacteria;p__Poribacteria;c__WGA-4E;o__GCA-2687025;f__GCA-2687025;g__VGLH01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009749465.1	s__Agromyces terreus	74.7711	55	1659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003014735.1	s__Actinosynnema carneum	74.6898	74	1659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	95.10	95.10	0.83	0.83	2	-
GCF_004135405.1	s__Agromyces protaetiae	74.6794	72	1659	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Agromyces	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 18:32:58,399] [INFO] GTDB search result was written to GCA_018665855.1_ASM1866585v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:32:58,399] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:32:58,403] [INFO] DFAST_QC result json was written to GCA_018665855.1_ASM1866585v1_genomic.fna/dqc_result.json
[2023-06-18 18:32:58,404] [INFO] DFAST_QC completed!
[2023-06-18 18:32:58,404] [INFO] Total running time: 0h1m38s