[2024-01-24 10:47:09,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,638] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,638] [INFO] DQC Reference Directory: /var/lib/cwl/stg386c8aa6-f0bc-449c-8f3e-637438056d26/dqc_reference
[2024-01-24 10:47:11,839] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,915] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,916] [INFO] Running command: gunzip -c /var/lib/cwl/stgc638e484-4ae7-4e4a-a761-3aa3ee218cb9/GCF_024172165.1_ASM2417216v1_genomic.fna.gz | prodigal -d GCF_024172165.1_ASM2417216v1_genomic.fna/cds.fna -a GCF_024172165.1_ASM2417216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:51,579] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:51,579] [INFO] Task started: HMMsearch
[2024-01-24 10:47:51,579] [INFO] Running command: hmmsearch --tblout GCF_024172165.1_ASM2417216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg386c8aa6-f0bc-449c-8f3e-637438056d26/dqc_reference/reference_markers.hmm GCF_024172165.1_ASM2417216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:52,067] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:52,069] [INFO] Found 6/6 markers.
[2024-01-24 10:47:52,168] [INFO] Query marker FASTA was written to GCF_024172165.1_ASM2417216v1_genomic.fna/markers.fasta
[2024-01-24 10:47:52,168] [INFO] Task started: Blastn
[2024-01-24 10:47:52,169] [INFO] Running command: blastn -query GCF_024172165.1_ASM2417216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg386c8aa6-f0bc-449c-8f3e-637438056d26/dqc_reference/reference_markers.fasta -out GCF_024172165.1_ASM2417216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:53,548] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:53,555] [INFO] Selected 17 target genomes.
[2024-01-24 10:47:53,555] [INFO] Target genome list was writen to GCF_024172165.1_ASM2417216v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:53,576] [INFO] Task started: fastANI
[2024-01-24 10:47:53,576] [INFO] Running command: fastANI --query /var/lib/cwl/stgc638e484-4ae7-4e4a-a761-3aa3ee218cb9/GCF_024172165.1_ASM2417216v1_genomic.fna.gz --refList GCF_024172165.1_ASM2417216v1_genomic.fna/target_genomes.txt --output GCF_024172165.1_ASM2417216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:48:48,947] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:48,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg386c8aa6-f0bc-449c-8f3e-637438056d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:48:48,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg386c8aa6-f0bc-449c-8f3e-637438056d26/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:48:48,965] [INFO] Found 17 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 10:48:48,966] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 10:48:48,966] [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
Nonomuraea rubra	strain=DSM 43768	GCA_014207985.1	46180	46180	type	True	93.347	3478	4586	95	below_threshold
Nonomuraea candida	strain=NRRL B-24552	GCA_000725485.1	359159	359159	type	True	88.1695	2706	4586	95	below_threshold
Nonomuraea fuscirosea	strain=CGMCC 4.7104	GCA_003001935.1	1291556	1291556	type	True	86.8195	2752	4586	95	below_threshold
Nonomuraea solani	strain=CGMCC 4.7037	GCA_900108335.1	1144553	1144553	type	True	86.5482	2876	4586	95	below_threshold
Nonomuraea zeae	strain=DSM 100528	GCA_005889725.1	1642303	1642303	type	True	86.1263	2796	4586	95	below_threshold
Nonomuraea jabiensis	strain=DSM 45507	GCA_014204795.1	882448	882448	type	True	85.6996	2740	4586	95	below_threshold
Nonomuraea terrae	strain=CH32	GCA_004348995.1	2530383	2530383	type	True	85.6468	2231	4586	95	below_threshold
Nonomuraea angiospora	strain=DSM 43173	GCA_014873145.1	46172	46172	type	True	85.6234	2719	4586	95	below_threshold
Nonomuraea aridisoli	strain=KC333	GCA_003236395.1	2070368	2070368	type	True	85.6016	2192	4586	95	below_threshold
Nonomuraea phyllanthi	strain=WYY166	GCA_009497075.1	2219224	2219224	type	True	85.5101	2474	4586	95	below_threshold
Nonomuraea turkmeniaca	strain=DSM 43926	GCA_005889735.1	103838	103838	type	True	85.4785	2346	4586	95	below_threshold
Nonomuraea phyllanthi	strain=PA1-10	GCA_006334985.2	2219224	2219224	type	True	85.453	2448	4586	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	85.3961	2561	4586	95	below_threshold
Nonomuraea cypriaca	strain=K274	GCA_015645445.1	1187855	1187855	type	True	85.3834	2251	4586	95	below_threshold
Nonomuraea rhizosphaerae	strain=CGMCC 4.7431	GCA_019396405.1	2665663	2665663	type	True	84.1237	1337	4586	95	below_threshold
Nonomuraea roseoviolacea subsp. carminata	strain=DSM 44170	GCA_024172185.1	160689	103837	type	True	83.0367	2110	4586	95	below_threshold
Nonomuraea montanisoli	strain=SMC 257	GCA_013363975.1	2741721	2741721	type	True	82.8384	2128	4586	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:48:48,968] [INFO] DFAST Taxonomy check result was written to GCF_024172165.1_ASM2417216v1_genomic.fna/tc_result.tsv
[2024-01-24 10:48:48,968] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:48:48,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:48:48,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg386c8aa6-f0bc-449c-8f3e-637438056d26/dqc_reference/checkm_data
[2024-01-24 10:48:48,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:48:49,088] [INFO] Task started: CheckM
[2024-01-24 10:48:49,088] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024172165.1_ASM2417216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024172165.1_ASM2417216v1_genomic.fna/checkm_input GCF_024172165.1_ASM2417216v1_genomic.fna/checkm_result
[2024-01-24 10:51:48,538] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:48,540] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 11.69%
Strain heterogeneity: 55.56%
--------------------------------------------------------------------------------
[2024-01-24 10:51:48,574] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:48,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:48,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024172165.1_ASM2417216v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:48,575] [INFO] Task started: Blastn
[2024-01-24 10:51:48,576] [INFO] Running command: blastn -query GCF_024172165.1_ASM2417216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg386c8aa6-f0bc-449c-8f3e-637438056d26/dqc_reference/reference_markers_gtdb.fasta -out GCF_024172165.1_ASM2417216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:50,694] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:50,699] [INFO] Selected 12 target genomes.
[2024-01-24 10:51:50,699] [INFO] Target genome list was writen to GCF_024172165.1_ASM2417216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:50,707] [INFO] Task started: fastANI
[2024-01-24 10:51:50,707] [INFO] Running command: fastANI --query /var/lib/cwl/stgc638e484-4ae7-4e4a-a761-3aa3ee218cb9/GCF_024172165.1_ASM2417216v1_genomic.fna.gz --refList GCF_024172165.1_ASM2417216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024172165.1_ASM2417216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:52:33,191] [INFO] Task succeeded: fastANI
[2024-01-24 10:52:33,203] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 10:52:33,203] [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_014207985.1	s__Nonomuraea rubra	93.3258	3482	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086045.1	s__Nonomuraea sp008086045	90.973	3365	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900323885.1	s__Nonomuraea parvosata	89.879	3225	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	98.64	97.29	0.94	0.90	3	-
GCF_000725485.1	s__Nonomuraea candida	88.1959	2702	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003001935.1	s__Nonomuraea fuscirosea	86.7999	2758	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889725.1	s__Nonomuraea zeae	86.1363	2795	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014204795.1	s__Nonomuraea jabiensis	85.67	2747	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003236395.1	s__Nonomuraea sp003236395	85.6009	2189	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005889735.1	s__Nonomuraea turkmeniaca	85.4617	2350	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005893125.1	s__Nonomuraea sp005893125	85.3952	2562	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363995.1	s__Nonomuraea rhodomycinica	83.0105	2131	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013363975.1	s__Nonomuraea montanisoli	82.8326	2128	4586	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nonomuraea	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:52:33,209] [INFO] GTDB search result was written to GCF_024172165.1_ASM2417216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:52:33,214] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:52:33,220] [INFO] DFAST_QC result json was written to GCF_024172165.1_ASM2417216v1_genomic.fna/dqc_result.json
[2024-01-24 10:52:33,221] [INFO] DFAST_QC completed!
[2024-01-24 10:52:33,221] [INFO] Total running time: 0h5m24s