[2024-01-24 13:40:40,129] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:40,131] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:40,131] [INFO] DQC Reference Directory: /var/lib/cwl/stg670ddf39-1fb9-4518-826d-3d815ef960be/dqc_reference
[2024-01-24 13:40:41,452] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:41,453] [INFO] Task started: Prodigal
[2024-01-24 13:40:41,453] [INFO] Running command: gunzip -c /var/lib/cwl/stgae1dcb99-840c-401c-8825-787d6362b214/GCF_027921805.1_ASM2792180v1_genomic.fna.gz | prodigal -d GCF_027921805.1_ASM2792180v1_genomic.fna/cds.fna -a GCF_027921805.1_ASM2792180v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:54,949] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:54,949] [INFO] Task started: HMMsearch
[2024-01-24 13:40:54,950] [INFO] Running command: hmmsearch --tblout GCF_027921805.1_ASM2792180v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg670ddf39-1fb9-4518-826d-3d815ef960be/dqc_reference/reference_markers.hmm GCF_027921805.1_ASM2792180v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:55,394] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:55,396] [INFO] Found 6/6 markers.
[2024-01-24 13:40:55,441] [INFO] Query marker FASTA was written to GCF_027921805.1_ASM2792180v1_genomic.fna/markers.fasta
[2024-01-24 13:40:55,442] [INFO] Task started: Blastn
[2024-01-24 13:40:55,442] [INFO] Running command: blastn -query GCF_027921805.1_ASM2792180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg670ddf39-1fb9-4518-826d-3d815ef960be/dqc_reference/reference_markers.fasta -out GCF_027921805.1_ASM2792180v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:56,731] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:56,734] [INFO] Selected 14 target genomes.
[2024-01-24 13:40:56,734] [INFO] Target genome list was writen to GCF_027921805.1_ASM2792180v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:56,740] [INFO] Task started: fastANI
[2024-01-24 13:40:56,740] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1dcb99-840c-401c-8825-787d6362b214/GCF_027921805.1_ASM2792180v1_genomic.fna.gz --refList GCF_027921805.1_ASM2792180v1_genomic.fna/target_genomes.txt --output GCF_027921805.1_ASM2792180v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,030] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,030] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg670ddf39-1fb9-4518-826d-3d815ef960be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,030] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg670ddf39-1fb9-4518-826d-3d815ef960be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,042] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:13,042] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,043] [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
Nocardioides luteus	strain=JCM 3358	GCA_014648595.1	1844	1844	type	True	99.9747	1618	1645	95	conclusive
Nocardioides albus	strain=JCM 3185	GCA_014648255.1	1841	1841	type	True	88.2911	1304	1645	95	below_threshold
Nocardioides panzhihuensis	strain=DSM 26487	GCA_013408335.1	860243	860243	type	True	88.1909	1341	1645	95	below_threshold
Nocardioides albertanoniae	strain=DSM 25218	GCA_006716315.1	1175486	1175486	type	True	87.3004	1281	1645	95	below_threshold
Nocardioides nematodiphilus	strain=R-N-C8	GCA_020216525.1	2849669	2849669	type	True	80.2859	646	1645	95	below_threshold
Nocardioides panaciterrulae	strain=DSM 21350	GCA_013409645.1	661492	661492	type	True	79.694	615	1645	95	below_threshold
Nocardioides baculatus	strain=G10	GCA_016735675.1	2801337	2801337	type	True	79.5597	613	1645	95	below_threshold
Nocardioides soli	strain=DSM 105498	GCA_014191495.1	1036020	1036020	type	True	79.5477	690	1645	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	79.4618	543	1645	95	below_threshold
Nocardioides malaquae	strain=Y6	GCA_015070385.1	2773426	2773426	type	True	79.4446	470	1645	95	below_threshold
Nocardioides sambongensis	strain=KUDC 5002	GCA_006494815.1	2589074	2589074	type	True	79.4089	642	1645	95	below_threshold
Nocardioides humilatus	strain=BN130099	GCA_008373755.1	2607660	2607660	type	True	79.4003	592	1645	95	below_threshold
Nocardioides ganghwensis	strain=9920	GCA_014779655.1	252230	252230	type	True	79.3249	638	1645	95	below_threshold
Nocardioides carbamazepini	strain=CBZ_1	GCA_024614185.1	2854259	2854259	type	True	79.213	687	1645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,045] [INFO] DFAST Taxonomy check result was written to GCF_027921805.1_ASM2792180v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,049] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,049] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,049] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg670ddf39-1fb9-4518-826d-3d815ef960be/dqc_reference/checkm_data
[2024-01-24 13:41:13,051] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,098] [INFO] Task started: CheckM
[2024-01-24 13:41:13,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_027921805.1_ASM2792180v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_027921805.1_ASM2792180v1_genomic.fna/checkm_input GCF_027921805.1_ASM2792180v1_genomic.fna/checkm_result
[2024-01-24 13:42:14,355] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:14,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:14,380] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:14,381] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:14,381] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_027921805.1_ASM2792180v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:14,381] [INFO] Task started: Blastn
[2024-01-24 13:42:14,382] [INFO] Running command: blastn -query GCF_027921805.1_ASM2792180v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg670ddf39-1fb9-4518-826d-3d815ef960be/dqc_reference/reference_markers_gtdb.fasta -out GCF_027921805.1_ASM2792180v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:16,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:16,330] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:16,330] [INFO] Target genome list was writen to GCF_027921805.1_ASM2792180v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:16,348] [INFO] Task started: fastANI
[2024-01-24 13:42:16,348] [INFO] Running command: fastANI --query /var/lib/cwl/stgae1dcb99-840c-401c-8825-787d6362b214/GCF_027921805.1_ASM2792180v1_genomic.fna.gz --refList GCF_027921805.1_ASM2792180v1_genomic.fna/target_genomes_gtdb.txt --output GCF_027921805.1_ASM2792180v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:30,438] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:30,456] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:42:30,456] [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_014648595.1	s__Nocardioides luteus	99.9747	1618	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000960475.2	s__Nocardioides luteus_A	89.2545	1323	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015752315.1	s__Nocardioides sp000192415	89.2078	1355	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	98.29	98.29	0.91	0.91	2	-
GCF_011045035.1	s__Nocardioides sp011045035	89.1131	1343	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715835.1	s__Nocardioides sp006715835	89.0295	1383	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009858265.1	s__Nocardioides sp009858265	89.0093	1353	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006715515.1	s__Nocardioides sp006715515	88.9656	1360	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101045.1	s__Nocardioides sp900101045	88.9323	1390	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014648255.1	s__Nocardioides albus	88.3019	1303	1645	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Propionibacteriales;f__Nocardioidaceae;g__Nocardioides	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:30,458] [INFO] GTDB search result was written to GCF_027921805.1_ASM2792180v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:30,459] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:30,464] [INFO] DFAST_QC result json was written to GCF_027921805.1_ASM2792180v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:30,464] [INFO] DFAST_QC completed!
[2024-01-24 13:42:30,464] [INFO] Total running time: 0h1m50s