[2024-01-24 14:39:45,005] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:45,007] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:45,007] [INFO] DQC Reference Directory: /var/lib/cwl/stg418c8f77-f3db-4372-b6b4-31813716af39/dqc_reference
[2024-01-24 14:39:46,506] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:46,515] [INFO] Task started: Prodigal
[2024-01-24 14:39:46,516] [INFO] Running command: gunzip -c /var/lib/cwl/stg37c1d23d-84e1-4f00-b11f-0f518e6e4171/GCF_002234385.1_ASM223438v1_genomic.fna.gz | prodigal -d GCF_002234385.1_ASM223438v1_genomic.fna/cds.fna -a GCF_002234385.1_ASM223438v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:40:16,461] [INFO] Task succeeded: Prodigal
[2024-01-24 14:40:16,462] [INFO] Task started: HMMsearch
[2024-01-24 14:40:16,462] [INFO] Running command: hmmsearch --tblout GCF_002234385.1_ASM223438v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg418c8f77-f3db-4372-b6b4-31813716af39/dqc_reference/reference_markers.hmm GCF_002234385.1_ASM223438v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:40:16,888] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:40:16,890] [INFO] Found 6/6 markers.
[2024-01-24 14:40:16,966] [INFO] Query marker FASTA was written to GCF_002234385.1_ASM223438v1_genomic.fna/markers.fasta
[2024-01-24 14:40:16,966] [INFO] Task started: Blastn
[2024-01-24 14:40:16,967] [INFO] Running command: blastn -query GCF_002234385.1_ASM223438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg418c8f77-f3db-4372-b6b4-31813716af39/dqc_reference/reference_markers.fasta -out GCF_002234385.1_ASM223438v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:18,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:18,345] [INFO] Selected 15 target genomes.
[2024-01-24 14:40:18,346] [INFO] Target genome list was writen to GCF_002234385.1_ASM223438v1_genomic.fna/target_genomes.txt
[2024-01-24 14:40:18,353] [INFO] Task started: fastANI
[2024-01-24 14:40:18,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg37c1d23d-84e1-4f00-b11f-0f518e6e4171/GCF_002234385.1_ASM223438v1_genomic.fna.gz --refList GCF_002234385.1_ASM223438v1_genomic.fna/target_genomes.txt --output GCF_002234385.1_ASM223438v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:40:58,340] [INFO] Task succeeded: fastANI
[2024-01-24 14:40:58,341] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg418c8f77-f3db-4372-b6b4-31813716af39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:40:58,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg418c8f77-f3db-4372-b6b4-31813716af39/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:40:58,356] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:40:58,356] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:40:58,356] [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
Amycolatopsis alba	strain=DSM 44262	GCA_002234385.1	76020	76020	type	True	100.0	3046	3058	95	conclusive
Amycolatopsis alba	strain=DSM 44262	GCA_000384215.1	76020	76020	type	True	99.9955	3057	3058	95	conclusive
Amycolatopsis azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	92.7571	2335	3058	95	below_threshold
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	92.7541	2375	3058	95	below_threshold
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	92.4261	2201	3058	95	below_threshold
Amycolatopsis umgeniensis	strain=DSM 45272	GCA_014205155.1	336628	336628	type	True	91.4825	2329	3058	95	below_threshold
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	90.8801	2241	3058	95	below_threshold
Amycolatopsis orientalis	strain=KCTC 9412	GCA_000478275.1	31958	31958	type	True	90.1151	2159	3058	95	below_threshold
Amycolatopsis regifaucium	strain=GY080	GCA_001613935.1	546365	546365	type	True	89.8019	2047	3058	95	below_threshold
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	89.7522	2061	3058	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.4747	1604	3058	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.7057	1064	3058	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	78.9222	979	3058	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.6342	960	3058	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.0465	788	3058	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:40:58,358] [INFO] DFAST Taxonomy check result was written to GCF_002234385.1_ASM223438v1_genomic.fna/tc_result.tsv
[2024-01-24 14:40:58,358] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:40:58,358] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:40:58,359] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg418c8f77-f3db-4372-b6b4-31813716af39/dqc_reference/checkm_data
[2024-01-24 14:40:58,360] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:40:58,444] [INFO] Task started: CheckM
[2024-01-24 14:40:58,444] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002234385.1_ASM223438v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002234385.1_ASM223438v1_genomic.fna/checkm_input GCF_002234385.1_ASM223438v1_genomic.fna/checkm_result
[2024-01-24 14:42:25,617] [INFO] Task succeeded: CheckM
[2024-01-24 14:42:25,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:42:25,647] [INFO] ===== Completeness check finished =====
[2024-01-24 14:42:25,647] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:42:25,648] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002234385.1_ASM223438v1_genomic.fna/markers.fasta)
[2024-01-24 14:42:25,648] [INFO] Task started: Blastn
[2024-01-24 14:42:25,648] [INFO] Running command: blastn -query GCF_002234385.1_ASM223438v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg418c8f77-f3db-4372-b6b4-31813716af39/dqc_reference/reference_markers_gtdb.fasta -out GCF_002234385.1_ASM223438v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:42:27,722] [INFO] Task succeeded: Blastn
[2024-01-24 14:42:27,725] [INFO] Selected 11 target genomes.
[2024-01-24 14:42:27,725] [INFO] Target genome list was writen to GCF_002234385.1_ASM223438v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:42:27,734] [INFO] Task started: fastANI
[2024-01-24 14:42:27,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg37c1d23d-84e1-4f00-b11f-0f518e6e4171/GCF_002234385.1_ASM223438v1_genomic.fna.gz --refList GCF_002234385.1_ASM223438v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002234385.1_ASM223438v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:42:55,865] [INFO] Task succeeded: fastANI
[2024-01-24 14:42:55,880] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:42:55,880] [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_000384215.1	s__Amycolatopsis alba	99.9955	3057	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014654365.1	s__Amycolatopsis oliviviridis	92.776	2353	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001995215.1	s__Amycolatopsis azurea	92.7397	2377	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002234405.1	s__Amycolatopsis thailandensis	92.3873	2206	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000342005.1	s__Amycolatopsis decaplanina	91.5968	2133	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205155.1	s__Amycolatopsis umgeniensis	91.4958	2326	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849735.1	s__Amycolatopsis sp002849735	91.3558	2329	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000732925.1	s__Amycolatopsis japonica	90.8988	2239	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.30	96.67	0.90	0.88	4	-
GCF_001620365.2	s__Amycolatopsis keratiniphila	90.7713	2185	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	97.78	96.67	0.89	0.86	5	-
GCF_000478275.1	s__Amycolatopsis orientalis	90.0781	2164	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	96.64	96.64	0.89	0.89	2	-
GCF_013870525.1	s__Amycolatopsis pittospori	89.7339	2064	3058	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:42:55,882] [INFO] GTDB search result was written to GCF_002234385.1_ASM223438v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:42:55,883] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:42:55,886] [INFO] DFAST_QC result json was written to GCF_002234385.1_ASM223438v1_genomic.fna/dqc_result.json
[2024-01-24 14:42:55,886] [INFO] DFAST_QC completed!
[2024-01-24 14:42:55,886] [INFO] Total running time: 0h3m11s