[2024-01-25 18:46:35,534] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:46:35,536] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:46:35,536] [INFO] DQC Reference Directory: /var/lib/cwl/stg394eea8e-4620-4871-ada5-b60ac28dad04/dqc_reference
[2024-01-25 18:46:36,740] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:46:36,741] [INFO] Task started: Prodigal
[2024-01-25 18:46:36,741] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc9c3d69-a180-4749-8cd7-f2c8d5cd5e3a/GCF_016862515.1_ASM1686251v1_genomic.fna.gz | prodigal -d GCF_016862515.1_ASM1686251v1_genomic.fna/cds.fna -a GCF_016862515.1_ASM1686251v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:46:57,450] [INFO] Task succeeded: Prodigal
[2024-01-25 18:46:57,451] [INFO] Task started: HMMsearch
[2024-01-25 18:46:57,451] [INFO] Running command: hmmsearch --tblout GCF_016862515.1_ASM1686251v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg394eea8e-4620-4871-ada5-b60ac28dad04/dqc_reference/reference_markers.hmm GCF_016862515.1_ASM1686251v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:46:57,823] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:46:57,824] [INFO] Found 6/6 markers.
[2024-01-25 18:46:57,889] [INFO] Query marker FASTA was written to GCF_016862515.1_ASM1686251v1_genomic.fna/markers.fasta
[2024-01-25 18:46:57,889] [INFO] Task started: Blastn
[2024-01-25 18:46:57,889] [INFO] Running command: blastn -query GCF_016862515.1_ASM1686251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg394eea8e-4620-4871-ada5-b60ac28dad04/dqc_reference/reference_markers.fasta -out GCF_016862515.1_ASM1686251v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:46:59,113] [INFO] Task succeeded: Blastn
[2024-01-25 18:46:59,116] [INFO] Selected 7 target genomes.
[2024-01-25 18:46:59,117] [INFO] Target genome list was writen to GCF_016862515.1_ASM1686251v1_genomic.fna/target_genomes.txt
[2024-01-25 18:46:59,120] [INFO] Task started: fastANI
[2024-01-25 18:46:59,121] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc9c3d69-a180-4749-8cd7-f2c8d5cd5e3a/GCF_016862515.1_ASM1686251v1_genomic.fna.gz --refList GCF_016862515.1_ASM1686251v1_genomic.fna/target_genomes.txt --output GCF_016862515.1_ASM1686251v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:47:15,952] [INFO] Task succeeded: fastANI
[2024-01-25 18:47:15,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg394eea8e-4620-4871-ada5-b60ac28dad04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:47:15,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg394eea8e-4620-4871-ada5-b60ac28dad04/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:47:15,958] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:47:15,959] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:47:15,959] [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
Asanoa iriomotensis	strain=NBRC 100142	GCA_016862515.1	234613	234613	type	True	100.0	2754	2759	95	conclusive
Asanoa siamensis	strain=NBRC 107932	GCA_016862555.1	926357	926357	type	True	87.6204	1960	2759	95	below_threshold
Asanoa hainanensis	strain=CGMCC 4.5593	GCA_900188485.1	560556	560556	type	True	86.7064	2018	2759	95	below_threshold
Asanoa ishikariensis	strain=NBRC 14551	GCA_016862535.1	137265	137265	type	True	86.5926	2033	2759	95	below_threshold
Asanoa ishikariensis	strain=DSM 44718	GCA_900107455.1	137265	137265	type	True	86.5517	2053	2759	95	below_threshold
Asanoa ferruginea	strain=DSM 44099	GCA_003387075.1	53367	53367	type	True	85.8895	2035	2759	95	below_threshold
Asanoa ferruginea	strain=NBRC 14496	GCA_016862495.1	53367	53367	type	True	85.8592	2013	2759	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:47:15,960] [INFO] DFAST Taxonomy check result was written to GCF_016862515.1_ASM1686251v1_genomic.fna/tc_result.tsv
[2024-01-25 18:47:15,961] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:47:15,961] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:47:15,961] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg394eea8e-4620-4871-ada5-b60ac28dad04/dqc_reference/checkm_data
[2024-01-25 18:47:15,962] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:47:16,039] [INFO] Task started: CheckM
[2024-01-25 18:47:16,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016862515.1_ASM1686251v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016862515.1_ASM1686251v1_genomic.fna/checkm_input GCF_016862515.1_ASM1686251v1_genomic.fna/checkm_result
[2024-01-25 18:48:24,132] [INFO] Task succeeded: CheckM
[2024-01-25 18:48:24,133] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:48:24,156] [INFO] ===== Completeness check finished =====
[2024-01-25 18:48:24,156] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:48:24,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016862515.1_ASM1686251v1_genomic.fna/markers.fasta)
[2024-01-25 18:48:24,158] [INFO] Task started: Blastn
[2024-01-25 18:48:24,158] [INFO] Running command: blastn -query GCF_016862515.1_ASM1686251v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg394eea8e-4620-4871-ada5-b60ac28dad04/dqc_reference/reference_markers_gtdb.fasta -out GCF_016862515.1_ASM1686251v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:48:26,049] [INFO] Task succeeded: Blastn
[2024-01-25 18:48:26,052] [INFO] Selected 7 target genomes.
[2024-01-25 18:48:26,052] [INFO] Target genome list was writen to GCF_016862515.1_ASM1686251v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:48:26,059] [INFO] Task started: fastANI
[2024-01-25 18:48:26,060] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc9c3d69-a180-4749-8cd7-f2c8d5cd5e3a/GCF_016862515.1_ASM1686251v1_genomic.fna.gz --refList GCF_016862515.1_ASM1686251v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016862515.1_ASM1686251v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:48:43,143] [INFO] Task succeeded: fastANI
[2024-01-25 18:48:43,149] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:48:43,149] [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_016862515.1	s__Asanoa iriomotensis	100.0	2754	2759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_016862555.1	s__Asanoa siamensis	87.5906	1966	2759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900188485.1	s__Asanoa hainanensis	86.6978	2020	2759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107455.1	s__Asanoa ishikariensis	86.5452	2054	2759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003387075.1	s__Asanoa ferruginea	85.8777	2038	2759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Asanoa	95.0	100.00	100.00	1.00	1.00	2	-
GCF_011764565.1	s__Phytohabitans suffuscus	79.5076	1327	2759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862915.1	s__Plantactinospora endophytica	79.4214	1245	2759	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Plantactinospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:48:43,151] [INFO] GTDB search result was written to GCF_016862515.1_ASM1686251v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:48:43,151] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:48:43,154] [INFO] DFAST_QC result json was written to GCF_016862515.1_ASM1686251v1_genomic.fna/dqc_result.json
[2024-01-25 18:48:43,154] [INFO] DFAST_QC completed!
[2024-01-25 18:48:43,154] [INFO] Total running time: 0h2m8s