[2024-01-24 14:11:45,512] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:11:45,514] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:11:45,514] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b3b8c4b-c5fd-406e-8926-b46d26e742a5/dqc_reference
[2024-01-24 14:11:46,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:11:46,729] [INFO] Task started: Prodigal
[2024-01-24 14:11:46,729] [INFO] Running command: gunzip -c /var/lib/cwl/stgab42de67-1061-4bef-9fd2-c9442d6f3084/GCF_000235425.2_ASM23542v3_genomic.fna.gz | prodigal -d GCF_000235425.2_ASM23542v3_genomic.fna/cds.fna -a GCF_000235425.2_ASM23542v3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:12:14,834] [INFO] Task succeeded: Prodigal
[2024-01-24 14:12:14,834] [INFO] Task started: HMMsearch
[2024-01-24 14:12:14,835] [INFO] Running command: hmmsearch --tblout GCF_000235425.2_ASM23542v3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b3b8c4b-c5fd-406e-8926-b46d26e742a5/dqc_reference/reference_markers.hmm GCF_000235425.2_ASM23542v3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:12:15,315] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:12:15,316] [INFO] Found 6/6 markers.
[2024-01-24 14:12:15,404] [INFO] Query marker FASTA was written to GCF_000235425.2_ASM23542v3_genomic.fna/markers.fasta
[2024-01-24 14:12:15,405] [INFO] Task started: Blastn
[2024-01-24 14:12:15,405] [INFO] Running command: blastn -query GCF_000235425.2_ASM23542v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3b8c4b-c5fd-406e-8926-b46d26e742a5/dqc_reference/reference_markers.fasta -out GCF_000235425.2_ASM23542v3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:12:16,770] [INFO] Task succeeded: Blastn
[2024-01-24 14:12:16,773] [INFO] Selected 11 target genomes.
[2024-01-24 14:12:16,774] [INFO] Target genome list was writen to GCF_000235425.2_ASM23542v3_genomic.fna/target_genomes.txt
[2024-01-24 14:12:16,779] [INFO] Task started: fastANI
[2024-01-24 14:12:16,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgab42de67-1061-4bef-9fd2-c9442d6f3084/GCF_000235425.2_ASM23542v3_genomic.fna.gz --refList GCF_000235425.2_ASM23542v3_genomic.fna/target_genomes.txt --output GCF_000235425.2_ASM23542v3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:12:44,321] [INFO] Task succeeded: fastANI
[2024-01-24 14:12:44,322] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b3b8c4b-c5fd-406e-8926-b46d26e742a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:12:44,323] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b3b8c4b-c5fd-406e-8926-b46d26e742a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:12:44,349] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:12:44,350] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:12:44,350] [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
Frankia saprophytica	strain=CN3	GCA_000235425.3	298655	298655	type	True	100.0	3325	3326	95	conclusive
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	89.2057	2253	3326	95	below_threshold
Frankia inefficax	strain=EuI1c	GCA_000166135.1	298654	298654	type	True	82.612	1847	3326	95	below_threshold
Frankia discariae	strain=BCU110501	GCA_000373365.1	365528	365528	type	True	78.7834	1196	3326	95	below_threshold
Frankia soli	strain=NRRL B-16219	GCA_001854695.1	2599596	2599596	type	True	78.7333	1150	3326	95	below_threshold
Frankia irregularis	strain=DSM 45899	GCA_001536285.1	795642	795642	type	True	78.5446	1215	3326	95	below_threshold
Frankia elaeagni	strain=BMG5.12	GCA_000374165.1	222534	222534	type	True	78.5008	1051	3326	95	below_threshold
Frankia alni	strain=ACN14a	GCA_000058485.1	1859	1859	type	True	78.4631	1106	3326	95	below_threshold
Frankia torreyi	strain=CpI1	GCA_000948395.1	1856	1856	type	True	78.3339	1107	3326	95	below_threshold
Actinomadura nitritigenes	strain=L46	GCA_017573545.1	134602	134602	type	True	76.0043	1019	3326	95	below_threshold
Actinomadura violacea	strain=LCR2-06	GCA_017573465.1	2819934	2819934	type	True	75.9476	1074	3326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:12:44,352] [INFO] DFAST Taxonomy check result was written to GCF_000235425.2_ASM23542v3_genomic.fna/tc_result.tsv
[2024-01-24 14:12:44,353] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:12:44,353] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:12:44,353] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b3b8c4b-c5fd-406e-8926-b46d26e742a5/dqc_reference/checkm_data
[2024-01-24 14:12:44,354] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:12:44,444] [INFO] Task started: CheckM
[2024-01-24 14:12:44,445] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000235425.2_ASM23542v3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000235425.2_ASM23542v3_genomic.fna/checkm_input GCF_000235425.2_ASM23542v3_genomic.fna/checkm_result
[2024-01-24 14:14:02,622] [INFO] Task succeeded: CheckM
[2024-01-24 14:14:02,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:14:02,652] [INFO] ===== Completeness check finished =====
[2024-01-24 14:14:02,652] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:14:02,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000235425.2_ASM23542v3_genomic.fna/markers.fasta)
[2024-01-24 14:14:02,653] [INFO] Task started: Blastn
[2024-01-24 14:14:02,653] [INFO] Running command: blastn -query GCF_000235425.2_ASM23542v3_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b3b8c4b-c5fd-406e-8926-b46d26e742a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000235425.2_ASM23542v3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:14:04,660] [INFO] Task succeeded: Blastn
[2024-01-24 14:14:04,665] [INFO] Selected 7 target genomes.
[2024-01-24 14:14:04,665] [INFO] Target genome list was writen to GCF_000235425.2_ASM23542v3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:14:04,678] [INFO] Task started: fastANI
[2024-01-24 14:14:04,679] [INFO] Running command: fastANI --query /var/lib/cwl/stgab42de67-1061-4bef-9fd2-c9442d6f3084/GCF_000235425.2_ASM23542v3_genomic.fna.gz --refList GCF_000235425.2_ASM23542v3_genomic.fna/target_genomes_gtdb.txt --output GCF_000235425.2_ASM23542v3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:14:27,724] [INFO] Task succeeded: fastANI
[2024-01-24 14:14:27,736] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:14:27,737] [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_000235425.2	s__Frankia saprophytica	100.0	3325	3326	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.94	99.94	1.00	1.00	2	conclusive
GCF_001854805.1	s__Frankia sp001854805	89.6357	2379	3326	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983105.1	s__Frankia asymbiotica	89.2288	2248	3326	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016786325.1	s__Frankia sp016786325	83.8432	2054	3326	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.95	99.95	0.97	0.97	3	-
GCF_000166135.1	s__Frankia inefficax	82.64	1838	3326	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016786355.1	s__Frankia sp016786355	82.5598	1786	3326	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.92	99.92	0.97	0.97	3	-
GCF_000966285.1	s__Frankia sp000966285	82.3313	1473	3326	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:14:27,739] [INFO] GTDB search result was written to GCF_000235425.2_ASM23542v3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:14:27,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:14:27,744] [INFO] DFAST_QC result json was written to GCF_000235425.2_ASM23542v3_genomic.fna/dqc_result.json
[2024-01-24 14:14:27,744] [INFO] DFAST_QC completed!
[2024-01-24 14:14:27,744] [INFO] Total running time: 0h2m42s