[2024-01-24 15:26:55,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:55,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:55,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg41e44db5-1505-48d5-a878-1d2b25e83e9f/dqc_reference
[2024-01-24 15:26:56,429] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:56,430] [INFO] Task started: Prodigal
[2024-01-24 15:26:56,430] [INFO] Running command: gunzip -c /var/lib/cwl/stg7140fe7e-48c8-419e-966f-4b27c5a07458/GCF_003202065.1_ASM320206v1_genomic.fna.gz | prodigal -d GCF_003202065.1_ASM320206v1_genomic.fna/cds.fna -a GCF_003202065.1_ASM320206v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:33,962] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:33,962] [INFO] Task started: HMMsearch
[2024-01-24 15:27:33,963] [INFO] Running command: hmmsearch --tblout GCF_003202065.1_ASM320206v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41e44db5-1505-48d5-a878-1d2b25e83e9f/dqc_reference/reference_markers.hmm GCF_003202065.1_ASM320206v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:34,337] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:34,338] [INFO] Found 6/6 markers.
[2024-01-24 15:27:34,409] [INFO] Query marker FASTA was written to GCF_003202065.1_ASM320206v1_genomic.fna/markers.fasta
[2024-01-24 15:27:34,409] [INFO] Task started: Blastn
[2024-01-24 15:27:34,409] [INFO] Running command: blastn -query GCF_003202065.1_ASM320206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41e44db5-1505-48d5-a878-1d2b25e83e9f/dqc_reference/reference_markers.fasta -out GCF_003202065.1_ASM320206v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:35,720] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:35,723] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:35,724] [INFO] Target genome list was writen to GCF_003202065.1_ASM320206v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:35,734] [INFO] Task started: fastANI
[2024-01-24 15:27:35,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg7140fe7e-48c8-419e-966f-4b27c5a07458/GCF_003202065.1_ASM320206v1_genomic.fna.gz --refList GCF_003202065.1_ASM320206v1_genomic.fna/target_genomes.txt --output GCF_003202065.1_ASM320206v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:59,804] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:59,805] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41e44db5-1505-48d5-a878-1d2b25e83e9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:59,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41e44db5-1505-48d5-a878-1d2b25e83e9f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:59,814] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:27:59,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:59,814] [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 tenerifensis	strain=DSM 44704	GCA_003202065.1	228006	228006	type	True	100.0	3250	3254	95	conclusive
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	99.8574	2904	3254	95	conclusive
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	87.1081	2276	3254	95	below_threshold
Nocardia suismassiliense	strain=S-137	GCA_900269665.1	2077092	2077092	type	True	86.7185	2147	3254	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	86.5727	2125	3254	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	86.0931	1946	3254	95	below_threshold
Nocardia brasiliensis	strain=NCTC11294	GCA_900454265.1	37326	37326	suspected-type	True	84.7982	2035	3254	95	below_threshold
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	84.7731	2021	3254	95	below_threshold
Nocardia vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	84.7393	2059	3254	95	below_threshold
Nocardia brasiliensis	strain=NBRC 14402	GCA_000308475.2	37326	37326	suspected-type	True	84.7032	1998	3254	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:59,816] [INFO] DFAST Taxonomy check result was written to GCF_003202065.1_ASM320206v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:59,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:59,816] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:59,816] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41e44db5-1505-48d5-a878-1d2b25e83e9f/dqc_reference/checkm_data
[2024-01-24 15:27:59,817] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:59,901] [INFO] Task started: CheckM
[2024-01-24 15:27:59,901] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003202065.1_ASM320206v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003202065.1_ASM320206v1_genomic.fna/checkm_input GCF_003202065.1_ASM320206v1_genomic.fna/checkm_result
[2024-01-24 15:29:37,120] [INFO] Task succeeded: CheckM
[2024-01-24 15:29:37,121] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.48%
Strain heterogeneity: 33.33%
--------------------------------------------------------------------------------
[2024-01-24 15:29:37,145] [INFO] ===== Completeness check finished =====
[2024-01-24 15:29:37,145] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:29:37,145] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003202065.1_ASM320206v1_genomic.fna/markers.fasta)
[2024-01-24 15:29:37,146] [INFO] Task started: Blastn
[2024-01-24 15:29:37,146] [INFO] Running command: blastn -query GCF_003202065.1_ASM320206v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41e44db5-1505-48d5-a878-1d2b25e83e9f/dqc_reference/reference_markers_gtdb.fasta -out GCF_003202065.1_ASM320206v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:29:39,056] [INFO] Task succeeded: Blastn
[2024-01-24 15:29:39,059] [INFO] Selected 11 target genomes.
[2024-01-24 15:29:39,059] [INFO] Target genome list was writen to GCF_003202065.1_ASM320206v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:29:39,067] [INFO] Task started: fastANI
[2024-01-24 15:29:39,067] [INFO] Running command: fastANI --query /var/lib/cwl/stg7140fe7e-48c8-419e-966f-4b27c5a07458/GCF_003202065.1_ASM320206v1_genomic.fna.gz --refList GCF_003202065.1_ASM320206v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003202065.1_ASM320206v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:30:05,983] [INFO] Task succeeded: fastANI
[2024-01-24 15:30:05,992] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:30:05,993] [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_000308715.1	s__Nocardia tenerifensis	99.8574	2904	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_008704205.1	s__Nocardia colli	87.1294	2273	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900269665.1	s__Nocardia suismassiliense	86.7209	2146	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.20	95.20	0.87	0.87	2	-
GCF_007990755.1	s__Nocardia ninae	86.583	2123	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	95.51	95.51	0.86	0.86	2	-
GCF_019222765.1	s__Nocardia iowensis	86.0704	1950	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613425.1	s__Nocardia vulneris	84.7759	2053	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
GCF_000308475.2	s__Nocardia brasiliensis	84.7114	1996	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	-
GCF_000250675.2	s__Nocardia brasiliensis_B	84.6396	2045	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	-
GCF_000710915.1	s__Nocardia brasiliensis_A	84.5939	1972	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_000308575.1	s__Nocardia exalbida	82.6084	1436	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_000308795.1	s__Nocardia thailandica	81.0651	1202	3254	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:30:05,994] [INFO] GTDB search result was written to GCF_003202065.1_ASM320206v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:30:05,995] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:30:05,998] [INFO] DFAST_QC result json was written to GCF_003202065.1_ASM320206v1_genomic.fna/dqc_result.json
[2024-01-24 15:30:05,998] [INFO] DFAST_QC completed!
[2024-01-24 15:30:05,998] [INFO] Total running time: 0h3m11s