[2024-01-24 10:49:33,633] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:49:33,636] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:49:33,636] [INFO] DQC Reference Directory: /var/lib/cwl/stg4505e6d9-c458-44fe-9cd6-3abb98d44e8b/dqc_reference
[2024-01-24 10:49:34,874] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:49:34,875] [INFO] Task started: Prodigal
[2024-01-24 10:49:34,875] [INFO] Running command: gunzip -c /var/lib/cwl/stg5b65e27b-fdc2-43b3-a4ab-53ddbfdb2e37/GCF_006716355.1_ASM671635v1_genomic.fna.gz | prodigal -d GCF_006716355.1_ASM671635v1_genomic.fna/cds.fna -a GCF_006716355.1_ASM671635v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:49:54,357] [INFO] Task succeeded: Prodigal
[2024-01-24 10:49:54,357] [INFO] Task started: HMMsearch
[2024-01-24 10:49:54,358] [INFO] Running command: hmmsearch --tblout GCF_006716355.1_ASM671635v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4505e6d9-c458-44fe-9cd6-3abb98d44e8b/dqc_reference/reference_markers.hmm GCF_006716355.1_ASM671635v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:49:54,716] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:49:54,718] [INFO] Found 6/6 markers.
[2024-01-24 10:49:54,765] [INFO] Query marker FASTA was written to GCF_006716355.1_ASM671635v1_genomic.fna/markers.fasta
[2024-01-24 10:49:54,765] [INFO] Task started: Blastn
[2024-01-24 10:49:54,765] [INFO] Running command: blastn -query GCF_006716355.1_ASM671635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4505e6d9-c458-44fe-9cd6-3abb98d44e8b/dqc_reference/reference_markers.fasta -out GCF_006716355.1_ASM671635v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:49:55,758] [INFO] Task succeeded: Blastn
[2024-01-24 10:49:55,763] [INFO] Selected 19 target genomes.
[2024-01-24 10:49:55,763] [INFO] Target genome list was writen to GCF_006716355.1_ASM671635v1_genomic.fna/target_genomes.txt
[2024-01-24 10:49:55,784] [INFO] Task started: fastANI
[2024-01-24 10:49:55,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b65e27b-fdc2-43b3-a4ab-53ddbfdb2e37/GCF_006716355.1_ASM671635v1_genomic.fna.gz --refList GCF_006716355.1_ASM671635v1_genomic.fna/target_genomes.txt --output GCF_006716355.1_ASM671635v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:50:18,677] [INFO] Task succeeded: fastANI
[2024-01-24 10:50:18,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4505e6d9-c458-44fe-9cd6-3abb98d44e8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:50:18,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4505e6d9-c458-44fe-9cd6-3abb98d44e8b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:50:18,698] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:50:18,698] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:50:18,698] [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
Stackebrandtia endophytica	strain=DSM 45928	GCA_006716355.1	1496996	1496996	type	True	100.0	1886	1887	95	conclusive
Stackebrandtia albiflava	strain=DSM 45044	GCA_007994225.1	406432	406432	type	True	79.8529	814	1887	95	below_threshold
Stackebrandtia nassauensis	strain=DSM 44728	GCA_000024545.1	283811	283811	type	True	78.6352	607	1887	95	below_threshold
Glycomyces xiaoerkulensis	strain=TRM 41368	GCA_002798405.1	2038139	2038139	type	True	77.3695	306	1887	95	below_threshold
Phytomonospora endophytica	strain=YIM 65646	GCA_014202425.1	714109	714109	type	True	77.2085	458	1887	95	below_threshold
Glycomyces salinus	strain=YIM 93776	GCA_016428645.1	980294	980294	type	True	77.203	317	1887	95	below_threshold
Micromonospora rhizosphaerae	strain=DSM 45431	GCA_900091465.1	568872	568872	type	True	76.8036	311	1887	95	below_threshold
Micromonospora veneta	strain=CAP181	GCA_016598485.1	2796464	2796464	type	True	76.798	304	1887	95	below_threshold
Micromonospora rosaria	strain=DSM 803	GCA_001567585.1	47874	47874	type	True	76.5655	322	1887	95	below_threshold
Catellatospora tritici	strain=NEAU-YM18	GCA_019083965.1	2851566	2851566	type	True	76.5438	348	1887	95	below_threshold
Actinoplanes cyaneus	strain=NBRC 14990	GCA_016862095.1	52696	52696	type	True	76.3756	310	1887	95	below_threshold
Rugosimonospora africana	strain=NBRC 104875	GCA_016862975.1	556532	556532	type	True	76.3224	319	1887	95	below_threshold
Streptacidiphilus melanogenes	strain=NBRC 103184	GCA_000787835.1	411235	411235	type	True	76.2287	245	1887	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	76.1777	246	1887	95	below_threshold
Saccharothrix australiensis	strain=DSM 43800	GCA_003634935.1	2072	2072	type	True	76.0718	253	1887	95	below_threshold
Dactylosporangium siamense	strain=NBRC 106093	GCA_016862795.1	685454	685454	type	True	76.0717	382	1887	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	76.0645	248	1887	95	below_threshold
Pseudonocardia thermophila	strain=DSM 43832	GCA_900142365.1	1848	1848	type	True	75.9013	206	1887	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:50:18,701] [INFO] DFAST Taxonomy check result was written to GCF_006716355.1_ASM671635v1_genomic.fna/tc_result.tsv
[2024-01-24 10:50:18,702] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:50:18,702] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:50:18,702] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4505e6d9-c458-44fe-9cd6-3abb98d44e8b/dqc_reference/checkm_data
[2024-01-24 10:50:18,704] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:50:18,757] [INFO] Task started: CheckM
[2024-01-24 10:50:18,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006716355.1_ASM671635v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006716355.1_ASM671635v1_genomic.fna/checkm_input GCF_006716355.1_ASM671635v1_genomic.fna/checkm_result
[2024-01-24 10:51:21,274] [INFO] Task succeeded: CheckM
[2024-01-24 10:51:21,275] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:51:21,303] [INFO] ===== Completeness check finished =====
[2024-01-24 10:51:21,303] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:51:21,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006716355.1_ASM671635v1_genomic.fna/markers.fasta)
[2024-01-24 10:51:21,304] [INFO] Task started: Blastn
[2024-01-24 10:51:21,304] [INFO] Running command: blastn -query GCF_006716355.1_ASM671635v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4505e6d9-c458-44fe-9cd6-3abb98d44e8b/dqc_reference/reference_markers_gtdb.fasta -out GCF_006716355.1_ASM671635v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:51:22,626] [INFO] Task succeeded: Blastn
[2024-01-24 10:51:22,631] [INFO] Selected 17 target genomes.
[2024-01-24 10:51:22,631] [INFO] Target genome list was writen to GCF_006716355.1_ASM671635v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:51:22,644] [INFO] Task started: fastANI
[2024-01-24 10:51:22,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg5b65e27b-fdc2-43b3-a4ab-53ddbfdb2e37/GCF_006716355.1_ASM671635v1_genomic.fna.gz --refList GCF_006716355.1_ASM671635v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006716355.1_ASM671635v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:51:43,185] [INFO] Task succeeded: fastANI
[2024-01-24 10:51:43,201] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:51:43,201] [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_006716355.1	s__Stackebrandtia endophytica	100.0	1886	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_007994225.1	s__Stackebrandtia albiflava	79.8618	816	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019113825.1	s__Stackebrandtia excrementipullorum	79.0455	638	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000024545.1	s__Stackebrandtia nassauensis	78.615	610	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202425.1	s__Phytomonospora endophytica	77.2394	453	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Phytomonospora	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019112895.1	s__Stackebrandtia faecavium	77.1852	224	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Stackebrandtia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000719515.1	s__Glycomyces sp000719515	77.0414	300	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Glycomyces	95.0	99.99	99.99	1.00	1.00	2	-
GCF_009712475.1	s__Micromonospora sp009712475	76.8105	296	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016598485.1	s__Micromonospora veneta	76.7907	305	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Micromonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019083965.1	s__Catellatospora sp019083965	76.538	348	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Catellatospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862095.1	s__Actinoplanes cyaneus	76.3767	311	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000715855.1	s__Actinoplanes liguriensis	76.3722	327	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Actinoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	76.1527	251	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341105.1	s__Nocardiopsis_A potens	76.0784	246	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016862795.1	s__Dactylosporangium siamense	76.0462	388	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Micromonosporaceae;g__Dactylosporangium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900142365.1	s__Pseudonocardia thermophila	75.8943	207	1887	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Pseudonocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017308975.1	s__Amycolatopsis sp017308975	75.807	284	1887	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 10:51:43,204] [INFO] GTDB search result was written to GCF_006716355.1_ASM671635v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:51:43,204] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:51:43,208] [INFO] DFAST_QC result json was written to GCF_006716355.1_ASM671635v1_genomic.fna/dqc_result.json
[2024-01-24 10:51:43,208] [INFO] DFAST_QC completed!
[2024-01-24 10:51:43,209] [INFO] Total running time: 0h2m10s