[2024-01-25 20:24:05,594] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:24:05,595] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:24:05,595] [INFO] DQC Reference Directory: /var/lib/cwl/stg15782360-202d-41a1-9580-aba4127d2671/dqc_reference
[2024-01-25 20:24:06,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:24:06,721] [INFO] Task started: Prodigal
[2024-01-25 20:24:06,721] [INFO] Running command: gunzip -c /var/lib/cwl/stge38dc0b5-23af-4e25-9035-631dc5d9ae39/GCF_014646215.1_ASM1464621v1_genomic.fna.gz | prodigal -d GCF_014646215.1_ASM1464621v1_genomic.fna/cds.fna -a GCF_014646215.1_ASM1464621v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:24:18,892] [INFO] Task succeeded: Prodigal
[2024-01-25 20:24:18,892] [INFO] Task started: HMMsearch
[2024-01-25 20:24:18,892] [INFO] Running command: hmmsearch --tblout GCF_014646215.1_ASM1464621v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15782360-202d-41a1-9580-aba4127d2671/dqc_reference/reference_markers.hmm GCF_014646215.1_ASM1464621v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:24:19,116] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:24:19,116] [INFO] Found 6/6 markers.
[2024-01-25 20:24:19,155] [INFO] Query marker FASTA was written to GCF_014646215.1_ASM1464621v1_genomic.fna/markers.fasta
[2024-01-25 20:24:19,155] [INFO] Task started: Blastn
[2024-01-25 20:24:19,155] [INFO] Running command: blastn -query GCF_014646215.1_ASM1464621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15782360-202d-41a1-9580-aba4127d2671/dqc_reference/reference_markers.fasta -out GCF_014646215.1_ASM1464621v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:24:20,321] [INFO] Task succeeded: Blastn
[2024-01-25 20:24:20,326] [INFO] Selected 15 target genomes.
[2024-01-25 20:24:20,326] [INFO] Target genome list was writen to GCF_014646215.1_ASM1464621v1_genomic.fna/target_genomes.txt
[2024-01-25 20:24:20,334] [INFO] Task started: fastANI
[2024-01-25 20:24:20,334] [INFO] Running command: fastANI --query /var/lib/cwl/stge38dc0b5-23af-4e25-9035-631dc5d9ae39/GCF_014646215.1_ASM1464621v1_genomic.fna.gz --refList GCF_014646215.1_ASM1464621v1_genomic.fna/target_genomes.txt --output GCF_014646215.1_ASM1464621v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:24:40,393] [INFO] Task succeeded: fastANI
[2024-01-25 20:24:40,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15782360-202d-41a1-9580-aba4127d2671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:24:40,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15782360-202d-41a1-9580-aba4127d2671/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:24:40,404] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:24:40,404] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:24:40,404] [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
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	100.0	1630	1632	95	conclusive
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	78.9717	617	1632	95	below_threshold
Nakamurella flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	78.7685	603	1632	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	78.6453	672	1632	95	below_threshold
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	78.5028	606	1632	95	below_threshold
Nakamurella lactea	strain=DSM 19367	GCA_000426645.1	459515	459515	type	True	78.0543	553	1632	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	78.0052	657	1632	95	below_threshold
Nakamurella aerolata	strain=DB0629	GCA_013002705.1	1656892	1656892	type	True	77.8357	466	1632	95	below_threshold
Actinokineospora terrae	strain=DSM 44260	GCA_900111175.1	155974	155974	type	True	77.0895	484	1632	95	below_threshold
Actinokineospora cianjurensis	strain=DSM 45657	GCA_003663795.1	585224	585224	type	True	76.9416	482	1632	95	below_threshold
Streptoalloteichus hindustanus	strain=DSM 44523	GCA_900129375.1	2017	2017	type	True	76.8962	537	1632	95	below_threshold
Pseudonocardia petroleophila	strain=CGMCC 4.1532	GCA_014235185.1	37331	37331	type	True	76.5438	574	1632	95	below_threshold
Pseudonocardia parietis	strain=DSM 45256	GCA_017876315.1	570936	570936	type	True	76.5188	576	1632	95	below_threshold
Amycolatopsis australiensis	strain=DSM 44671	GCA_900119165.1	546364	546364	type	True	76.4934	638	1632	95	below_threshold
Amycolatopsis vancoresmycina	strain=NRRL B-24208	GCA_000716785.1	208444	208444	type	True	76.4175	629	1632	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:24:40,408] [INFO] DFAST Taxonomy check result was written to GCF_014646215.1_ASM1464621v1_genomic.fna/tc_result.tsv
[2024-01-25 20:24:40,410] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:24:40,410] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:24:40,410] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15782360-202d-41a1-9580-aba4127d2671/dqc_reference/checkm_data
[2024-01-25 20:24:40,411] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:24:40,461] [INFO] Task started: CheckM
[2024-01-25 20:24:40,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014646215.1_ASM1464621v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014646215.1_ASM1464621v1_genomic.fna/checkm_input GCF_014646215.1_ASM1464621v1_genomic.fna/checkm_result
[2024-01-25 20:26:10,680] [INFO] Task succeeded: CheckM
[2024-01-25 20:26:10,681] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:26:10,700] [INFO] ===== Completeness check finished =====
[2024-01-25 20:26:10,700] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:26:10,701] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014646215.1_ASM1464621v1_genomic.fna/markers.fasta)
[2024-01-25 20:26:10,701] [INFO] Task started: Blastn
[2024-01-25 20:26:10,701] [INFO] Running command: blastn -query GCF_014646215.1_ASM1464621v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg15782360-202d-41a1-9580-aba4127d2671/dqc_reference/reference_markers_gtdb.fasta -out GCF_014646215.1_ASM1464621v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:26:12,485] [INFO] Task succeeded: Blastn
[2024-01-25 20:26:12,489] [INFO] Selected 14 target genomes.
[2024-01-25 20:26:12,489] [INFO] Target genome list was writen to GCF_014646215.1_ASM1464621v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:26:12,503] [INFO] Task started: fastANI
[2024-01-25 20:26:12,503] [INFO] Running command: fastANI --query /var/lib/cwl/stge38dc0b5-23af-4e25-9035-631dc5d9ae39/GCF_014646215.1_ASM1464621v1_genomic.fna.gz --refList GCF_014646215.1_ASM1464621v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014646215.1_ASM1464621v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:26:28,840] [INFO] Task succeeded: fastANI
[2024-01-25 20:26:28,849] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:26:28,849] [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_014646215.1	s__Nakamurella endophytica	100.0	1630	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_009707545.1	s__Nakamurella sp009707545	79.5557	787	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918035.1	s__Nakamurella sp016918035	78.9002	627	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918095.1	s__Nakamurella flavida	78.7434	607	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024365.1	s__Nakamurella multipartita	78.6345	679	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005298075.1	s__Nakamurella flava	78.5499	598	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014303395.1	s__Nakamurella sp014303395	78.4025	564	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104535.1	s__Nakamurella panacisegetis	78.3792	616	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003260015.1	s__Nakamurella deserti	78.0148	655	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013002705.1	s__Nakamurella aerolata	77.8724	461	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111175.1	s__Actinokineospora terrae	77.0676	489	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinokineospora	95.0	95.61	95.61	0.89	0.89	2	-
GCA_000620205.1	s__Modestobacter sp000620205	76.7405	550	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Geodermatophilaceae;g__Modestobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002796545.1	s__Amycolatopsis sp002796545	76.5879	506	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	99.98	99.98	1.00	1.00	2	-
GCA_017882655.1	s__Fen-668 sp017882655	75.7155	129	1632	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Propionibacteriaceae;g__Fen-668	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:26:28,850] [INFO] GTDB search result was written to GCF_014646215.1_ASM1464621v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:26:28,851] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:26:28,853] [INFO] DFAST_QC result json was written to GCF_014646215.1_ASM1464621v1_genomic.fna/dqc_result.json
[2024-01-25 20:26:28,854] [INFO] DFAST_QC completed!
[2024-01-25 20:26:28,854] [INFO] Total running time: 0h2m23s