[2024-01-24 15:27:22,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:22,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:22,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg8748c7b8-511f-4e79-9f73-18cfc68bccc3/dqc_reference
[2024-01-24 15:27:23,485] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,487] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,488] [INFO] Running command: gunzip -c /var/lib/cwl/stga1fe538c-7ab6-46a4-9140-ee93f734198d/GCF_001618405.1_ASM161840v1_genomic.fna.gz | prodigal -d GCF_001618405.1_ASM161840v1_genomic.fna/cds.fna -a GCF_001618405.1_ASM161840v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:59,622] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:59,623] [INFO] Task started: HMMsearch
[2024-01-24 15:27:59,623] [INFO] Running command: hmmsearch --tblout GCF_001618405.1_ASM161840v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8748c7b8-511f-4e79-9f73-18cfc68bccc3/dqc_reference/reference_markers.hmm GCF_001618405.1_ASM161840v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:59,960] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:59,962] [INFO] Found 6/6 markers.
[2024-01-24 15:28:00,024] [INFO] Query marker FASTA was written to GCF_001618405.1_ASM161840v1_genomic.fna/markers.fasta
[2024-01-24 15:28:00,025] [INFO] Task started: Blastn
[2024-01-24 15:28:00,025] [INFO] Running command: blastn -query GCF_001618405.1_ASM161840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8748c7b8-511f-4e79-9f73-18cfc68bccc3/dqc_reference/reference_markers.fasta -out GCF_001618405.1_ASM161840v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:01,126] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:01,130] [INFO] Selected 16 target genomes.
[2024-01-24 15:28:01,130] [INFO] Target genome list was writen to GCF_001618405.1_ASM161840v1_genomic.fna/target_genomes.txt
[2024-01-24 15:28:01,137] [INFO] Task started: fastANI
[2024-01-24 15:28:01,137] [INFO] Running command: fastANI --query /var/lib/cwl/stga1fe538c-7ab6-46a4-9140-ee93f734198d/GCF_001618405.1_ASM161840v1_genomic.fna.gz --refList GCF_001618405.1_ASM161840v1_genomic.fna/target_genomes.txt --output GCF_001618405.1_ASM161840v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:28:28,036] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:28,037] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8748c7b8-511f-4e79-9f73-18cfc68bccc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:28:28,037] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8748c7b8-511f-4e79-9f73-18cfc68bccc3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:28:28,056] [INFO] Found 16 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:28:28,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:28:28,057] [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
Nocardia arizonensis	strain=NBRC 108935	GCA_001618405.1	1141647	1141647	type	True	100.0	2354	2357	95	conclusive
Nocardia arizonensis	strain=W9405	GCA_001310275.1	1141647	1141647	type	True	99.9699	2311	2357	95	conclusive
Nocardia takedensis	strain=NBRC 100417	GCA_000308695.1	259390	259390	type	True	84.5797	1488	2357	95	below_threshold
Nocardia bovistercoris	strain=NEAU-351	GCA_015674855.1	2785916	2785916	type	True	84.3753	1530	2357	95	below_threshold
Nocardia noduli	strain=ncl1	GCA_019038455.1	2815722	2815722	type	True	82.8117	1378	2357	95	below_threshold
Nocardia aurea	strain=SYSU K10002	GCA_003123685.1	2144174	2144174	type	True	82.4801	1453	2357	95	below_threshold
Nocardia amikacinitolerans	strain=NBRC 108937	GCA_001612615.1	756689	756689	type	True	81.9162	1211	2357	95	below_threshold
Nocardia amikacinitolerans	strain=DSM 45539	GCA_024172045.1	756689	756689	type	True	81.8699	1239	2357	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	81.8668	1233	2357	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	81.7604	1210	2357	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	81.1235	1164	2357	95	below_threshold
Nocardia higoensis	strain=NBRC 100133	GCA_000308595.1	228599	228599	type	True	81.0857	1086	2357	95	below_threshold
Nocardia africana	strain=FDAARGOS_1597	GCA_020731565.1	134964	134964	type	True	79.7124	969	2357	95	below_threshold
Nocardia africana	strain=NBRC 100379	GCA_001612635.1	134964	134964	type	True	79.6783	962	2357	95	below_threshold
Nocardia veterana	strain=NBRC 100344	GCA_000308855.1	132249	132249	type	True	79.3971	877	2357	95	below_threshold
Actinokineospora diospyrosa	strain=DSM 44255	GCA_024171925.1	103728	103728	type	True	76.3996	451	2357	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:28:28,058] [INFO] DFAST Taxonomy check result was written to GCF_001618405.1_ASM161840v1_genomic.fna/tc_result.tsv
[2024-01-24 15:28:28,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:28:28,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:28:28,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8748c7b8-511f-4e79-9f73-18cfc68bccc3/dqc_reference/checkm_data
[2024-01-24 15:28:28,060] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:28:28,145] [INFO] Task started: CheckM
[2024-01-24 15:28:28,145] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001618405.1_ASM161840v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001618405.1_ASM161840v1_genomic.fna/checkm_input GCF_001618405.1_ASM161840v1_genomic.fna/checkm_result
[2024-01-24 15:30:01,478] [INFO] Task succeeded: CheckM
[2024-01-24 15:30:01,480] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:30:01,506] [INFO] ===== Completeness check finished =====
[2024-01-24 15:30:01,507] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:30:01,508] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001618405.1_ASM161840v1_genomic.fna/markers.fasta)
[2024-01-24 15:30:01,509] [INFO] Task started: Blastn
[2024-01-24 15:30:01,509] [INFO] Running command: blastn -query GCF_001618405.1_ASM161840v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8748c7b8-511f-4e79-9f73-18cfc68bccc3/dqc_reference/reference_markers_gtdb.fasta -out GCF_001618405.1_ASM161840v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:30:03,040] [INFO] Task succeeded: Blastn
[2024-01-24 15:30:03,043] [INFO] Selected 18 target genomes.
[2024-01-24 15:30:03,043] [INFO] Target genome list was writen to GCF_001618405.1_ASM161840v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:30:03,054] [INFO] Task started: fastANI
[2024-01-24 15:30:03,054] [INFO] Running command: fastANI --query /var/lib/cwl/stga1fe538c-7ab6-46a4-9140-ee93f734198d/GCF_001618405.1_ASM161840v1_genomic.fna.gz --refList GCF_001618405.1_ASM161840v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001618405.1_ASM161840v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:32,617] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:32,643] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:32,644] [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_001310275.1	s__Nocardia arizonensis	99.9699	2311	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.98	99.98	0.99	0.99	2	conclusive
GCF_000308695.1	s__Nocardia takedensis	84.5907	1487	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015674855.1	s__Nocardia bovistercoris	84.4081	1524	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003123685.1	s__Nocardia aurea	82.4554	1459	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.19	95.19	0.76	0.76	2	-
GCF_001612615.1	s__Nocardia amikacinitolerans	81.925	1210	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.80	97.80	0.89	0.89	2	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	81.8803	1231	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613365.1	s__Nocardia xishanensis	81.7945	1209	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	81.7725	1208	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001182745.1	s__Nocardia farcinica	81.6479	1130	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.16	98.59	0.93	0.88	42	-
GCF_000308555.1	s__Nocardia cyriacigeorgica	81.3462	985	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.94	96.19	0.91	0.88	19	-
GCF_000308435.1	s__Nocardia araoensis	81.1739	1106	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612785.1	s__Nocardia beijingensis	81.1202	1163	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_000308595.1	s__Nocardia higoensis	81.0532	1090	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008704205.1	s__Nocardia colli	80.6622	1165	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612635.1	s__Nocardia africana	79.6876	960	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.93	99.93	0.99	0.99	2	-
GCF_000308855.1	s__Nocardia veterana	79.4006	877	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_009604425.1	s__Nocardia sp009604425	79.2808	935	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016464305.1	s__REN6 sp016464305	76.397	420	2357	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Pseudonocardiaceae;g__REN6	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:32,646] [INFO] GTDB search result was written to GCF_001618405.1_ASM161840v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:32,646] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:32,666] [INFO] DFAST_QC result json was written to GCF_001618405.1_ASM161840v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:32,667] [INFO] DFAST_QC completed!
[2024-01-24 15:30:32,667] [INFO] Total running time: 0h3m10s