[2024-01-24 13:17:41,705] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:41,707] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:41,707] [INFO] DQC Reference Directory: /var/lib/cwl/stg841d4d6c-6192-4248-ab8c-b039a44d4cea/dqc_reference
[2024-01-24 13:17:42,941] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:42,942] [INFO] Task started: Prodigal
[2024-01-24 13:17:42,942] [INFO] Running command: gunzip -c /var/lib/cwl/stgde6627b2-0e5f-4769-95a2-0e249066acde/GCF_000328705.1_ASM32870v1_genomic.fna.gz | prodigal -d GCF_000328705.1_ASM32870v1_genomic.fna/cds.fna -a GCF_000328705.1_ASM32870v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:19,590] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:19,591] [INFO] Task started: HMMsearch
[2024-01-24 13:18:19,591] [INFO] Running command: hmmsearch --tblout GCF_000328705.1_ASM32870v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg841d4d6c-6192-4248-ab8c-b039a44d4cea/dqc_reference/reference_markers.hmm GCF_000328705.1_ASM32870v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:19,967] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:19,969] [INFO] Found 6/6 markers.
[2024-01-24 13:18:20,041] [INFO] Query marker FASTA was written to GCF_000328705.1_ASM32870v1_genomic.fna/markers.fasta
[2024-01-24 13:18:20,042] [INFO] Task started: Blastn
[2024-01-24 13:18:20,042] [INFO] Running command: blastn -query GCF_000328705.1_ASM32870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841d4d6c-6192-4248-ab8c-b039a44d4cea/dqc_reference/reference_markers.fasta -out GCF_000328705.1_ASM32870v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:21,481] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:21,487] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:21,488] [INFO] Target genome list was writen to GCF_000328705.1_ASM32870v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:21,531] [INFO] Task started: fastANI
[2024-01-24 13:18:21,531] [INFO] Running command: fastANI --query /var/lib/cwl/stgde6627b2-0e5f-4769-95a2-0e249066acde/GCF_000328705.1_ASM32870v1_genomic.fna.gz --refList GCF_000328705.1_ASM32870v1_genomic.fna/target_genomes.txt --output GCF_000328705.1_ASM32870v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:52,144] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:52,145] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg841d4d6c-6192-4248-ab8c-b039a44d4cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:52,145] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg841d4d6c-6192-4248-ab8c-b039a44d4cea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:52,159] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:52,159] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:52,159] [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
Saccharothrix espanaensis	strain=type strain: DSM 44229	GCA_000328705.1	103731	103731	type	True	100.0	3120	3120	95	conclusive
Saccharothrix tamanrassetensis	strain=CECT 8640	GCA_014203665.1	1051531	1051531	type	True	86.4262	2041	3120	95	below_threshold
Saccharothrix algeriensis	strain=DSM 44581	GCA_016907655.1	173560	173560	type	True	85.5873	1740	3120	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	85.259	1849	3120	95	below_threshold
Saccharothrix obliqua	strain=SC076	GCA_019375475.1	2861747	2861747	type	True	85.0581	1847	3120	95	below_threshold
Saccharothrix variisporea	strain=DSM 43911	GCA_003634995.1	543527	543527	type	True	84.303	1843	3120	95	below_threshold
Saccharothrix saharensis	strain=DSM 45456	GCA_006716745.1	571190	571190	type	True	83.5412	1772	3120	95	below_threshold
Saccharothrix syringae	strain=NRRL B-16468	GCA_009498035.1	103733	103733	type	True	83.0367	1859	3120	95	below_threshold
Saccharothrix violaceirubra	strain=DSM 45084	GCA_014203755.1	413306	413306	type	True	82.2511	1517	3120	95	below_threshold
Lentzea tibetensis	strain=FXJ1.1311	GCA_007845675.1	2591470	2591470	type	True	80.1956	1377	3120	95	below_threshold
Lentzea californiensis	strain=DSM 43393	GCA_024648825.1	438851	438851	type	True	79.7505	1371	3120	95	below_threshold
Amycolatopsis acidiphila	strain=KCTC 39523	GCA_021391495.1	715473	715473	type	True	78.2128	968	3120	95	below_threshold
Prauserella aidingensis	strain=DSM 45266	GCA_024171865.1	387890	387890	type	True	77.5155	711	3120	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:52,161] [INFO] DFAST Taxonomy check result was written to GCF_000328705.1_ASM32870v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:52,162] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:52,162] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:52,162] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg841d4d6c-6192-4248-ab8c-b039a44d4cea/dqc_reference/checkm_data
[2024-01-24 13:18:52,163] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:52,251] [INFO] Task started: CheckM
[2024-01-24 13:18:52,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000328705.1_ASM32870v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000328705.1_ASM32870v1_genomic.fna/checkm_input GCF_000328705.1_ASM32870v1_genomic.fna/checkm_result
[2024-01-24 13:22:19,678] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:19,679] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:19,706] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:19,706] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:19,707] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000328705.1_ASM32870v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:19,707] [INFO] Task started: Blastn
[2024-01-24 13:22:19,707] [INFO] Running command: blastn -query GCF_000328705.1_ASM32870v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg841d4d6c-6192-4248-ab8c-b039a44d4cea/dqc_reference/reference_markers_gtdb.fasta -out GCF_000328705.1_ASM32870v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:21,944] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:21,948] [INFO] Selected 11 target genomes.
[2024-01-24 13:22:21,949] [INFO] Target genome list was writen to GCF_000328705.1_ASM32870v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:21,976] [INFO] Task started: fastANI
[2024-01-24 13:22:21,976] [INFO] Running command: fastANI --query /var/lib/cwl/stgde6627b2-0e5f-4769-95a2-0e249066acde/GCF_000328705.1_ASM32870v1_genomic.fna.gz --refList GCF_000328705.1_ASM32870v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000328705.1_ASM32870v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:22:51,136] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:51,157] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:22:51,158] [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_000328705.1	s__Actinosynnema espanaense	100.0	3120	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014203665.1	s__Actinosynnema tamanrassetense	86.4624	2035	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907655.1	s__Actinosynnema algeriensis	85.6303	1733	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634935.1	s__Actinosynnema australiense	85.2636	1850	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003634995.1	s__Actinosynnema variisporeum	84.2669	1848	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006716745.1	s__Actinosynnema saharense	83.6255	1754	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003752005.1	s__Actinosynnema texasense	83.5968	1786	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	98.51	98.51	0.92	0.92	2	-
GCF_001280085.1	s__Actinosynnema sp001280085	83.3417	1826	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009769385.1	s__Actinosynnema deserti	83.2646	1736	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009498035.1	s__Actinosynnema syringae	83.0971	1851	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	99.98	99.98	1.00	1.00	2	-
GCF_014203755.1	s__Actinosynnema violaceirubrum	82.2594	1512	3120	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Actinosynnema	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:22:51,160] [INFO] GTDB search result was written to GCF_000328705.1_ASM32870v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:22:51,161] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:22:51,165] [INFO] DFAST_QC result json was written to GCF_000328705.1_ASM32870v1_genomic.fna/dqc_result.json
[2024-01-24 13:22:51,165] [INFO] DFAST_QC completed!
[2024-01-24 13:22:51,166] [INFO] Total running time: 0h5m9s