[2024-01-24 11:20:49,933] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:20:49,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:20:49,935] [INFO] DQC Reference Directory: /var/lib/cwl/stgba8bee69-7911-425b-b75b-ee776991f0c1/dqc_reference
[2024-01-24 11:20:51,130] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:20:51,131] [INFO] Task started: Prodigal
[2024-01-24 11:20:51,131] [INFO] Running command: gunzip -c /var/lib/cwl/stge5a8c792-0f31-4392-a134-713142c00f37/GCF_010122465.1_ASM1012246v1_genomic.fna.gz | prodigal -d GCF_010122465.1_ASM1012246v1_genomic.fna/cds.fna -a GCF_010122465.1_ASM1012246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:21:11,152] [INFO] Task succeeded: Prodigal
[2024-01-24 11:21:11,153] [INFO] Task started: HMMsearch
[2024-01-24 11:21:11,153] [INFO] Running command: hmmsearch --tblout GCF_010122465.1_ASM1012246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba8bee69-7911-425b-b75b-ee776991f0c1/dqc_reference/reference_markers.hmm GCF_010122465.1_ASM1012246v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:21:11,504] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:21:11,506] [INFO] Found 6/6 markers.
[2024-01-24 11:21:11,566] [INFO] Query marker FASTA was written to GCF_010122465.1_ASM1012246v1_genomic.fna/markers.fasta
[2024-01-24 11:21:11,566] [INFO] Task started: Blastn
[2024-01-24 11:21:11,567] [INFO] Running command: blastn -query GCF_010122465.1_ASM1012246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba8bee69-7911-425b-b75b-ee776991f0c1/dqc_reference/reference_markers.fasta -out GCF_010122465.1_ASM1012246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:12,544] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:12,548] [INFO] Selected 21 target genomes.
[2024-01-24 11:21:12,548] [INFO] Target genome list was writen to GCF_010122465.1_ASM1012246v1_genomic.fna/target_genomes.txt
[2024-01-24 11:21:12,557] [INFO] Task started: fastANI
[2024-01-24 11:21:12,558] [INFO] Running command: fastANI --query /var/lib/cwl/stge5a8c792-0f31-4392-a134-713142c00f37/GCF_010122465.1_ASM1012246v1_genomic.fna.gz --refList GCF_010122465.1_ASM1012246v1_genomic.fna/target_genomes.txt --output GCF_010122465.1_ASM1012246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:21:37,490] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:37,491] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba8bee69-7911-425b-b75b-ee776991f0c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:21:37,491] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba8bee69-7911-425b-b75b-ee776991f0c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:21:37,513] [INFO] Found 21 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:21:37,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:21:37,513] [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
Phytoactinopolyspora mesophila	strain=XMNu-373	GCA_010122465.1	2650750	2650750	type	True	100.0	2156	2157	95	conclusive
Phytoactinopolyspora limicola	strain=HAJB-30	GCA_011320225.1	2715536	2715536	type	True	79.7117	878	2157	95	below_threshold
Phytoactinopolyspora alkaliphila	strain=CGMCC 4.7225	GCA_010550695.1	1783498	1783498	type	True	78.7465	703	2157	95	below_threshold
Phytoactinopolyspora endophytica	strain=EGI 60009	GCA_004138495.1	1642495	1642495	type	True	78.3286	690	2157	95	below_threshold
Phytoactinopolyspora halotolerans	strain=CCTCC AB 2017055	GCA_010550675.1	1981512	1981512	type	True	78.2971	759	2157	95	below_threshold
Phytoactinopolyspora halophila	strain=YIM 96934	GCA_003287285.1	1981511	1981511	type	True	77.8586	522	2157	95	below_threshold
Jiangella gansuensis	strain=DSM 44835	GCA_000515395.1	281473	281473	type	True	77.8397	535	2157	95	below_threshold
Jiangella aurantiaca	strain=8K307	GCA_004349105.1	2530373	2530373	type	True	77.6503	576	2157	95	below_threshold
Jiangella rhizosphaerae	strain=NEAU-YY265	GCA_003579925.1	2293569	2293569	type	True	77.6067	570	2157	95	below_threshold
Jiangella asiatica	strain=5K138	GCA_004349065.1	2530372	2530372	type	True	77.5647	552	2157	95	below_threshold
Jiangella ureilytica	strain=KC603	GCA_004348545.1	2530374	2530374	type	True	77.5482	529	2157	95	below_threshold
Jiangella alkaliphila	strain=DSM 45079	GCA_900105925.1	419479	419479	type	True	77.5191	577	2157	95	below_threshold
Jiangella alba	strain=YIM 61503	GCA_001708125.1	561176	561176	type	True	77.3202	646	2157	95	below_threshold
Jiangella alba	strain=DSM 45237	GCA_900106035.1	561176	561176	type	True	77.3035	645	2157	95	below_threshold
Motilibacter deserti	strain=E257	GCA_011250635.1	2714956	2714956	type	True	76.0815	220	2157	95	below_threshold
Nocardioides anomalus	strain=HKS04	GCA_011046535.1	2712223	2712223	type	True	76.0696	236	2157	95	below_threshold
Streptomyces harenosi	strain=PRKS01-65	GCA_011008945.1	2697029	2697029	type	True	76.0315	254	2157	95	below_threshold
Nonomuraea basaltis	strain=160415	GCA_005893125.1	2495887	2495887	type	True	75.9324	327	2157	95	below_threshold
Streptomyces daqingensis	strain=CGMCC 4.7178	GCA_014645895.1	1472640	1472640	type	True	75.8296	174	2157	95	below_threshold
Ornithinimicrobium sediminis	strain=EGI L100131	GCA_021272345.1	2904603	2904603	type	True	75.8192	152	2157	95	below_threshold
Actinomadura parmotrematis	strain=PM05-2	GCA_019458805.1	2864039	2864039	type	True	75.7687	287	2157	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:21:37,515] [INFO] DFAST Taxonomy check result was written to GCF_010122465.1_ASM1012246v1_genomic.fna/tc_result.tsv
[2024-01-24 11:21:37,516] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:21:37,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:21:37,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba8bee69-7911-425b-b75b-ee776991f0c1/dqc_reference/checkm_data
[2024-01-24 11:21:37,518] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:21:37,581] [INFO] Task started: CheckM
[2024-01-24 11:21:37,581] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010122465.1_ASM1012246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010122465.1_ASM1012246v1_genomic.fna/checkm_input GCF_010122465.1_ASM1012246v1_genomic.fna/checkm_result
[2024-01-24 11:22:35,789] [INFO] Task succeeded: CheckM
[2024-01-24 11:22:35,791] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:22:35,811] [INFO] ===== Completeness check finished =====
[2024-01-24 11:22:35,811] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:22:35,812] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010122465.1_ASM1012246v1_genomic.fna/markers.fasta)
[2024-01-24 11:22:35,812] [INFO] Task started: Blastn
[2024-01-24 11:22:35,812] [INFO] Running command: blastn -query GCF_010122465.1_ASM1012246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba8bee69-7911-425b-b75b-ee776991f0c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_010122465.1_ASM1012246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:22:37,227] [INFO] Task succeeded: Blastn
[2024-01-24 11:22:37,231] [INFO] Selected 15 target genomes.
[2024-01-24 11:22:37,231] [INFO] Target genome list was writen to GCF_010122465.1_ASM1012246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:22:37,245] [INFO] Task started: fastANI
[2024-01-24 11:22:37,245] [INFO] Running command: fastANI --query /var/lib/cwl/stge5a8c792-0f31-4392-a134-713142c00f37/GCF_010122465.1_ASM1012246v1_genomic.fna.gz --refList GCF_010122465.1_ASM1012246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010122465.1_ASM1012246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:22:57,774] [INFO] Task succeeded: fastANI
[2024-01-24 11:22:57,790] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:22:57,790] [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_010122465.1	s__Phytoactinopolyspora mesophila	100.0	2156	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_011320225.1	s__Phytoactinopolyspora limicola	79.7141	878	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010550695.1	s__Phytoactinopolyspora alkaliphila	78.7562	702	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010550675.1	s__Phytoactinopolyspora halotolerans	78.2979	760	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003287285.1	s__Phytoactinopolyspora halophila	77.86	522	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Phytoactinopolyspora	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000515395.1	s__Jiangella gansuensis	77.8522	533	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349105.1	s__Jiangella aurantiaca	77.6509	576	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003579925.1	s__Jiangella rhizosphaerae	77.6064	570	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004349065.1	s__Jiangella asiatica	77.5706	551	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004348545.1	s__Jiangella ureilytica	77.5502	528	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105925.1	s__Jiangella alkaliphila	77.4987	581	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900106035.1	s__Jiangella alba	77.2864	649	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	97.52	95.05	0.93	0.86	3	-
GCF_003427025.1	s__Jiangella endophytica	77.2694	585	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Jiangellales;f__Jiangellaceae;g__Jiangella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011046535.1	s__Nocardioides anomalus	76.0596	236	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014645895.1	s__Streptomyces daqingensis	75.8369	173	2157	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	95.38	95.38	0.92	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:22:57,792] [INFO] GTDB search result was written to GCF_010122465.1_ASM1012246v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:22:57,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:22:57,796] [INFO] DFAST_QC result json was written to GCF_010122465.1_ASM1012246v1_genomic.fna/dqc_result.json
[2024-01-24 11:22:57,797] [INFO] DFAST_QC completed!
[2024-01-24 11:22:57,797] [INFO] Total running time: 0h2m8s