[2024-01-24 11:19:54,426] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:19:54,434] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:19:54,434] [INFO] DQC Reference Directory: /var/lib/cwl/stgd86bfba5-7452-4283-bbd0-56a0f6a12540/dqc_reference
[2024-01-24 11:19:55,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:19:55,817] [INFO] Task started: Prodigal
[2024-01-24 11:19:55,818] [INFO] Running command: gunzip -c /var/lib/cwl/stg81647532-613c-48ad-9875-bfc0889215ab/GCF_006717075.1_ASM671707v1_genomic.fna.gz | prodigal -d GCF_006717075.1_ASM671707v1_genomic.fna/cds.fna -a GCF_006717075.1_ASM671707v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:20:10,785] [INFO] Task succeeded: Prodigal
[2024-01-24 11:20:10,785] [INFO] Task started: HMMsearch
[2024-01-24 11:20:10,786] [INFO] Running command: hmmsearch --tblout GCF_006717075.1_ASM671707v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd86bfba5-7452-4283-bbd0-56a0f6a12540/dqc_reference/reference_markers.hmm GCF_006717075.1_ASM671707v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:20:11,086] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:20:11,087] [INFO] Found 6/6 markers.
[2024-01-24 11:20:11,127] [INFO] Query marker FASTA was written to GCF_006717075.1_ASM671707v1_genomic.fna/markers.fasta
[2024-01-24 11:20:11,128] [INFO] Task started: Blastn
[2024-01-24 11:20:11,128] [INFO] Running command: blastn -query GCF_006717075.1_ASM671707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd86bfba5-7452-4283-bbd0-56a0f6a12540/dqc_reference/reference_markers.fasta -out GCF_006717075.1_ASM671707v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:20:12,144] [INFO] Task succeeded: Blastn
[2024-01-24 11:20:12,147] [INFO] Selected 20 target genomes.
[2024-01-24 11:20:12,148] [INFO] Target genome list was writen to GCF_006717075.1_ASM671707v1_genomic.fna/target_genomes.txt
[2024-01-24 11:20:12,156] [INFO] Task started: fastANI
[2024-01-24 11:20:12,156] [INFO] Running command: fastANI --query /var/lib/cwl/stg81647532-613c-48ad-9875-bfc0889215ab/GCF_006717075.1_ASM671707v1_genomic.fna.gz --refList GCF_006717075.1_ASM671707v1_genomic.fna/target_genomes.txt --output GCF_006717075.1_ASM671707v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:20:34,418] [INFO] Task succeeded: fastANI
[2024-01-24 11:20:34,419] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd86bfba5-7452-4283-bbd0-56a0f6a12540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:20:34,420] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd86bfba5-7452-4283-bbd0-56a0f6a12540/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:20:34,439] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:20:34,439] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:20:34,439] [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
Nocardiopsis gilva	strain=YIM 90087	GCA_002263495.1	280236	280236	type	True	79.5987	703	1643	95	below_threshold
Nocardiopsis gilva	strain=YIM 90087	GCA_000341165.1	280236	280236	type	True	79.5906	638	1643	95	below_threshold
Streptomonospora salina	strain=DSM 44593	GCA_014204715.1	104205	104205	type	True	79.5845	633	1643	95	below_threshold
Nocardiopsis mwathae	strain=DSM 46659	GCA_014201195.1	1472723	1472723	type	True	79.4892	718	1643	95	below_threshold
Streptomonospora litoralis	strain=M2	GCA_004323735.1	2498135	2498135	type	True	79.2579	652	1643	95	below_threshold
Streptomonospora alba	strain=YIM 90003	GCA_000826685.1	183763	183763	type	True	79.2279	653	1643	95	below_threshold
Nocardiopsis chromatogenes	strain=YIM 90109	GCA_000341185.1	280239	280239	type	True	79.1587	693	1643	95	below_threshold
Nocardiopsis composta	strain=DSM 44551	GCA_014200805.1	157465	157465	type	True	79.1411	745	1643	95	below_threshold
Nocardiopsis potens	strain=DSM 45234	GCA_000341105.1	1246458	1246458	type	True	79.0375	743	1643	95	below_threshold
Thermobifida halotolerans	strain=DSM 44931	GCA_003574835.2	483545	483545	type	True	78.8	562	1643	95	below_threshold
Thermobifida alba	strain=DSM 43795	GCA_023208015.1	53522	53522	type	True	78.7586	571	1643	95	below_threshold
Nocardiopsis sinuspersici	strain=UTMC 00102	GCA_001998325.1	501010	501010	type	True	78.7118	590	1643	95	below_threshold
Thermobifida halotolerans	strain=YIM 90462	GCA_001660385.1	483545	483545	type	True	78.6678	550	1643	95	below_threshold
Nocardiopsis dassonvillei	strain=NCTC10488	GCA_900638215.1	2014	2014	type	True	78.6094	605	1643	95	below_threshold
Nocardiopsis dassonvillei subsp. dassonvillei	strain=DSM 43111	GCA_000092985.1	568208	2014	type	True	78.5819	584	1643	95	below_threshold
Nocardiopsis dassonvillei	strain=ATCC 23218	GCA_012396345.1	2014	2014	type	True	78.4211	591	1643	95	below_threshold
Nocardiopsis dassonvillei subsp. crassaminis	strain=D1	GCA_902825375.1	2580523	2014	type	True	78.3658	540	1643	95	below_threshold
Nocardiopsis alborubida	strain=ATCC 23612	GCA_012396365.1	146802	146802	type	True	78.3611	592	1643	95	below_threshold
Nocardiopsis exhalans	strain=JCM11759T	GCA_024134545.1	163604	163604	type	True	78.3439	562	1643	95	below_threshold
Nonomuraea endophytica	strain=DSM 45385	GCA_014203235.1	714136	714136	type	True	76.2349	358	1643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:20:34,441] [INFO] DFAST Taxonomy check result was written to GCF_006717075.1_ASM671707v1_genomic.fna/tc_result.tsv
[2024-01-24 11:20:34,441] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:20:34,441] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:20:34,442] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd86bfba5-7452-4283-bbd0-56a0f6a12540/dqc_reference/checkm_data
[2024-01-24 11:20:34,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:20:34,490] [INFO] Task started: CheckM
[2024-01-24 11:20:34,490] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006717075.1_ASM671707v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006717075.1_ASM671707v1_genomic.fna/checkm_input GCF_006717075.1_ASM671707v1_genomic.fna/checkm_result
[2024-01-24 11:21:20,151] [INFO] Task succeeded: CheckM
[2024-01-24 11:21:20,152] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:21:20,172] [INFO] ===== Completeness check finished =====
[2024-01-24 11:21:20,172] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:21:20,173] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006717075.1_ASM671707v1_genomic.fna/markers.fasta)
[2024-01-24 11:21:20,173] [INFO] Task started: Blastn
[2024-01-24 11:21:20,173] [INFO] Running command: blastn -query GCF_006717075.1_ASM671707v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd86bfba5-7452-4283-bbd0-56a0f6a12540/dqc_reference/reference_markers_gtdb.fasta -out GCF_006717075.1_ASM671707v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:21:21,635] [INFO] Task succeeded: Blastn
[2024-01-24 11:21:21,639] [INFO] Selected 17 target genomes.
[2024-01-24 11:21:21,639] [INFO] Target genome list was writen to GCF_006717075.1_ASM671707v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:21:21,673] [INFO] Task started: fastANI
[2024-01-24 11:21:21,674] [INFO] Running command: fastANI --query /var/lib/cwl/stg81647532-613c-48ad-9875-bfc0889215ab/GCF_006717075.1_ASM671707v1_genomic.fna.gz --refList GCF_006717075.1_ASM671707v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006717075.1_ASM671707v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:21:41,742] [INFO] Task succeeded: fastANI
[2024-01-24 11:21:41,763] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:21:41,763] [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_006717075.1	s__Haloactinospora alba	100.0	1638	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Haloactinospora	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002263495.1	s__Nocardiopsis_C gilva	79.5907	706	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	99.97	99.97	1.00	1.00	2	-
GCF_014201195.1	s__Nocardiopsis_C mwathae	79.4847	714	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_C	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013408795.1	s__Spinactinospora alkalitolerans	79.4828	700	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Spinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341245.1	s__Nocardiopsis_A halophila	79.3579	671	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_A	95.0	98.23	98.23	0.90	0.90	2	-
GCF_009728995.1	s__Streptomonospora sp009728995	79.2754	665	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000981225.1	s__Allosalinactinospora lopnorensis	79.2611	675	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Allosalinactinospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004323735.1	s__Streptomonospora sp004323735	79.241	651	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013410565.1	s__Streptomonospora nanhaiensis	79.2404	712	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	99.69	99.69	0.95	0.95	2	-
GCF_000826685.1	s__Streptomonospora alba	79.2354	652	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Streptomonospora	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014200805.1	s__Nocardiopsis_A composta	79.1284	747	1643	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_000341185.1	s__Nocardiopsis_A chromatogenes	79.1249	697	1643	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_001552555.1	s__Nocardiopsis_B trehalosi	79.0975	687	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000341105.1	s__Nocardiopsis_A potens	79.0407	742	1643	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_001660385.1	s__Thermobifida halotolerans	78.6678	550	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Thermobifida	95.0	99.91	99.91	0.97	0.97	2	-
GCF_000092985.1	s__Nocardiopsis dassonvillei	78.5797	589	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	97.80	95.11	0.93	0.87	11	-
GCF_009830945.1	s__Nocardiopsis sp009830945	78.509	592	1643	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis	95.0	99.72	99.66	0.93	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:21:41,765] [INFO] GTDB search result was written to GCF_006717075.1_ASM671707v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:21:41,765] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:21:41,769] [INFO] DFAST_QC result json was written to GCF_006717075.1_ASM671707v1_genomic.fna/dqc_result.json
[2024-01-24 11:21:41,769] [INFO] DFAST_QC completed!
[2024-01-24 11:21:41,769] [INFO] Total running time: 0h1m47s