[2024-01-25 18:07:50,324] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:07:50,326] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:07:50,326] [INFO] DQC Reference Directory: /var/lib/cwl/stg658edb50-1f56-483b-853d-ece3de1de9e1/dqc_reference
[2024-01-25 18:07:51,482] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:07:51,482] [INFO] Task started: Prodigal
[2024-01-25 18:07:51,483] [INFO] Running command: gunzip -c /var/lib/cwl/stg72c8dc35-1c9f-42bf-a52a-18767432916b/GCF_000340415.1_Amycolatopsis_azurea_genomic.fna.gz | prodigal -d GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/cds.fna -a GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:14,414] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:14,415] [INFO] Task started: HMMsearch
[2024-01-25 18:08:14,415] [INFO] Running command: hmmsearch --tblout GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg658edb50-1f56-483b-853d-ece3de1de9e1/dqc_reference/reference_markers.hmm GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:14,756] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:14,757] [INFO] Found 6/6 markers.
[2024-01-25 18:08:14,823] [INFO] Query marker FASTA was written to GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/markers.fasta
[2024-01-25 18:08:14,823] [INFO] Task started: Blastn
[2024-01-25 18:08:14,823] [INFO] Running command: blastn -query GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/markers.fasta -db /var/lib/cwl/stg658edb50-1f56-483b-853d-ece3de1de9e1/dqc_reference/reference_markers.fasta -out GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:16,038] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:16,041] [INFO] Selected 15 target genomes.
[2024-01-25 18:08:16,041] [INFO] Target genome list was writen to GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/target_genomes.txt
[2024-01-25 18:08:16,055] [INFO] Task started: fastANI
[2024-01-25 18:08:16,055] [INFO] Running command: fastANI --query /var/lib/cwl/stg72c8dc35-1c9f-42bf-a52a-18767432916b/GCF_000340415.1_Amycolatopsis_azurea_genomic.fna.gz --refList GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/target_genomes.txt --output GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:50,883] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:50,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg658edb50-1f56-483b-853d-ece3de1de9e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:50,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg658edb50-1f56-483b-853d-ece3de1de9e1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:50,894] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:08:50,894] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:50,894] [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 azurea	strain=DSM 43854	GCA_000340415.1	36819	36819	type	True	100.0	2995	3002	95	conclusive
Amycolatopsis azurea	strain=DSM 43854	GCA_001995215.1	36819	36819	type	True	99.9953	2986	3002	95	conclusive
Amycolatopsis thailandensis	strain=JCM 16380	GCA_002234405.1	589330	589330	type	True	93.6198	2326	3002	95	below_threshold
Amycolatopsis alba	strain=DSM 44262	GCA_000384215.1	76020	76020	type	True	92.8687	2477	3002	95	below_threshold
Amycolatopsis alba	strain=DSM 44262	GCA_002234385.1	76020	76020	type	True	92.8218	2319	3002	95	below_threshold
Amycolatopsis umgeniensis	strain=DSM 45272	GCA_014205155.1	336628	336628	type	True	91.5966	2469	3002	95	below_threshold
Amycolatopsis japonica	strain=MG417-CF17	GCA_000732925.1	208439	208439	type	True	91.3098	2402	3002	95	below_threshold
Amycolatopsis keratiniphila subsp. nogabecina	strain=FH 1893	GCA_001953855.1	208442	129921	type	True	91.0986	2351	3002	95	below_threshold
Amycolatopsis keratiniphila subsp. keratiniphila	strain=DSM 44409	GCA_001620365.2	227715	129921	type	True	91.0797	2357	3002	95	below_threshold
Amycolatopsis pittospori	strain=PIP199	GCA_013870525.1	2749434	2749434	type	True	89.8877	2189	3002	95	below_threshold
Amycolatopsis camponoti	strain=A23	GCA_902497555.1	2606593	2606593	type	True	81.6705	1683	3002	95	below_threshold
Amycolatopsis thermalba	strain=NRRL B-24845	GCA_003385215.1	944492	944492	type	True	79.9975	1089	3002	95	below_threshold
Prauserella cavernicola	strain=ASG 168	GCA_016595675.1	2800127	2800127	type	True	79.0027	1005	3002	95	below_threshold
Amycolatopsis aidingensis	strain=YIM 96748	GCA_018885265.1	2842453	2842453	type	True	78.7146	1016	3002	95	below_threshold
Actinokineospora globicatena	strain=DSM 44256	GCA_024171945.1	103729	103729	type	True	78.0976	819	3002	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:50,896] [INFO] DFAST Taxonomy check result was written to GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/tc_result.tsv
[2024-01-25 18:08:50,896] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:50,896] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:50,897] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg658edb50-1f56-483b-853d-ece3de1de9e1/dqc_reference/checkm_data
[2024-01-25 18:08:50,897] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:50,980] [INFO] Task started: CheckM
[2024-01-25 18:08:50,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/checkm_input GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/checkm_result
[2024-01-25 18:10:10,872] [INFO] Task succeeded: CheckM
[2024-01-25 18:10:10,873] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:10:10,893] [INFO] ===== Completeness check finished =====
[2024-01-25 18:10:10,894] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:10:10,895] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/markers.fasta)
[2024-01-25 18:10:10,895] [INFO] Task started: Blastn
[2024-01-25 18:10:10,895] [INFO] Running command: blastn -query GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/markers.fasta -db /var/lib/cwl/stg658edb50-1f56-483b-853d-ece3de1de9e1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:10:12,846] [INFO] Task succeeded: Blastn
[2024-01-25 18:10:12,849] [INFO] Selected 10 target genomes.
[2024-01-25 18:10:12,849] [INFO] Target genome list was writen to GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:10:12,859] [INFO] Task started: fastANI
[2024-01-25 18:10:12,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg72c8dc35-1c9f-42bf-a52a-18767432916b/GCF_000340415.1_Amycolatopsis_azurea_genomic.fna.gz --refList GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/target_genomes_gtdb.txt --output GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:10:39,843] [INFO] Task succeeded: fastANI
[2024-01-25 18:10:39,850] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:10:39,850] [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_001995215.1	s__Amycolatopsis azurea	99.9953	2986	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_014654365.1	s__Amycolatopsis oliviviridis	93.9609	2542	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002234405.1	s__Amycolatopsis thailandensis	93.6271	2324	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000384215.1	s__Amycolatopsis alba	92.8515	2480	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000342005.1	s__Amycolatopsis decaplanina	91.8916	2256	3002	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	91.5862	2471	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000732925.1	s__Amycolatopsis japonica	91.3002	2403	3002	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	91.0822	2356	3002	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	90.3178	2251	3002	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	89.8877	2189	3002	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__Amycolatopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:10:39,852] [INFO] GTDB search result was written to GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/result_gtdb.tsv
[2024-01-25 18:10:39,852] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:10:39,855] [INFO] DFAST_QC result json was written to GCF_000340415.1_Amycolatopsis_azurea_genomic.fna/dqc_result.json
[2024-01-25 18:10:39,855] [INFO] DFAST_QC completed!
[2024-01-25 18:10:39,855] [INFO] Total running time: 0h2m50s