[2024-01-24 11:50:49,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:50:49,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:50:49,833] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c2ddaa7-902f-4759-a7e9-5387c6a02ac7/dqc_reference
[2024-01-24 11:50:51,037] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:50:51,038] [INFO] Task started: Prodigal
[2024-01-24 11:50:51,038] [INFO] Running command: gunzip -c /var/lib/cwl/stg7665a236-5ce2-4f4e-9ad3-13b8e9786274/GCF_016918095.1_ASM1691809v1_genomic.fna.gz | prodigal -d GCF_016918095.1_ASM1691809v1_genomic.fna/cds.fna -a GCF_016918095.1_ASM1691809v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:03,396] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:03,396] [INFO] Task started: HMMsearch
[2024-01-24 11:51:03,397] [INFO] Running command: hmmsearch --tblout GCF_016918095.1_ASM1691809v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c2ddaa7-902f-4759-a7e9-5387c6a02ac7/dqc_reference/reference_markers.hmm GCF_016918095.1_ASM1691809v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:03,684] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:03,686] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7665a236-5ce2-4f4e-9ad3-13b8e9786274/GCF_016918095.1_ASM1691809v1_genomic.fna.gz]
[2024-01-24 11:51:03,727] [INFO] Query marker FASTA was written to GCF_016918095.1_ASM1691809v1_genomic.fna/markers.fasta
[2024-01-24 11:51:03,728] [INFO] Task started: Blastn
[2024-01-24 11:51:03,728] [INFO] Running command: blastn -query GCF_016918095.1_ASM1691809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c2ddaa7-902f-4759-a7e9-5387c6a02ac7/dqc_reference/reference_markers.fasta -out GCF_016918095.1_ASM1691809v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:04,949] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:04,953] [INFO] Selected 10 target genomes.
[2024-01-24 11:51:04,954] [INFO] Target genome list was writen to GCF_016918095.1_ASM1691809v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:04,962] [INFO] Task started: fastANI
[2024-01-24 11:51:04,963] [INFO] Running command: fastANI --query /var/lib/cwl/stg7665a236-5ce2-4f4e-9ad3-13b8e9786274/GCF_016918095.1_ASM1691809v1_genomic.fna.gz --refList GCF_016918095.1_ASM1691809v1_genomic.fna/target_genomes.txt --output GCF_016918095.1_ASM1691809v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:16,338] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:16,339] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c2ddaa7-902f-4759-a7e9-5387c6a02ac7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:16,340] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c2ddaa7-902f-4759-a7e9-5387c6a02ac7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:16,353] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:16,353] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:16,353] [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 flavida	strain=KCTC 19127	GCA_016918095.1	363630	363630	type	True	100.0	1384	1411	95	conclusive
Nakamurella leprariae	strain=YIM 132084	GCA_016918035.1	2803911	2803911	type	True	79.9259	628	1411	95	below_threshold
Nakamurella flava	strain=N5BH11	GCA_005298075.1	2576308	2576308	type	True	79.3977	613	1411	95	below_threshold
Nakamurella multipartita	strain=DSM 44233	GCA_000024365.1	53461	53461	type	True	79.2767	627	1411	95	below_threshold
Nakamurella deserti	strain=12Sc4-1	GCA_003260015.1	2164074	2164074	type	True	78.9068	587	1411	95	below_threshold
Nakamurella endophytica	strain=CGMCC 4.7308	GCA_014646215.1	1748367	1748367	type	True	78.7959	614	1411	95	below_threshold
Nakamurella lactea	strain=DSM 19367	GCA_000426645.1	459515	459515	type	True	77.8288	470	1411	95	below_threshold
Crossiella cryophila	strain=DSM 44230	GCA_014204915.1	43355	43355	type	True	76.8248	479	1411	95	below_threshold
Pseudonocardia spinosispora	strain=DSM 44797	GCA_000429025.1	103441	103441	type	True	76.7303	381	1411	95	below_threshold
Actinomycetospora corticicola	strain=DSM 45772	GCA_013409505.1	663602	663602	type	True	76.6481	407	1411	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:16,356] [INFO] DFAST Taxonomy check result was written to GCF_016918095.1_ASM1691809v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:16,356] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:16,357] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:16,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c2ddaa7-902f-4759-a7e9-5387c6a02ac7/dqc_reference/checkm_data
[2024-01-24 11:51:16,359] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:16,403] [INFO] Task started: CheckM
[2024-01-24 11:51:16,404] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016918095.1_ASM1691809v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016918095.1_ASM1691809v1_genomic.fna/checkm_input GCF_016918095.1_ASM1691809v1_genomic.fna/checkm_result
[2024-01-24 11:52:24,521] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:24,522] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 8.33%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:24,549] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:24,550] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:24,550] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016918095.1_ASM1691809v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:24,550] [INFO] Task started: Blastn
[2024-01-24 11:52:24,551] [INFO] Running command: blastn -query GCF_016918095.1_ASM1691809v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c2ddaa7-902f-4759-a7e9-5387c6a02ac7/dqc_reference/reference_markers_gtdb.fasta -out GCF_016918095.1_ASM1691809v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:26,451] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:26,455] [INFO] Selected 10 target genomes.
[2024-01-24 11:52:26,456] [INFO] Target genome list was writen to GCF_016918095.1_ASM1691809v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:26,475] [INFO] Task started: fastANI
[2024-01-24 11:52:26,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg7665a236-5ce2-4f4e-9ad3-13b8e9786274/GCF_016918095.1_ASM1691809v1_genomic.fna.gz --refList GCF_016918095.1_ASM1691809v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016918095.1_ASM1691809v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:38,020] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:38,034] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:38,034] [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_016918095.1	s__Nakamurella flavida	100.0	1395	1411	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_016918035.1	s__Nakamurella sp016918035	79.9245	627	1411	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	79.4051	611	1411	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	79.2098	636	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009707545.1	s__Nakamurella sp009707545	79.0463	621	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646215.1	s__Nakamurella endophytica	78.8485	607	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003576535.1	s__Nakamurella silvestris	78.2818	437	1411	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	78.1607	480	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017882715.1	s__Nakamurella sp017882715	78.0128	387	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Nakamurellaceae;g__Nakamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013409505.1	s__Actinomycetospora corticicola	76.6584	405	1411	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinomycetospora	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:38,036] [INFO] GTDB search result was written to GCF_016918095.1_ASM1691809v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:38,037] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:38,040] [INFO] DFAST_QC result json was written to GCF_016918095.1_ASM1691809v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:38,040] [INFO] DFAST_QC completed!
[2024-01-24 11:52:38,040] [INFO] Total running time: 0h1m48s