[2024-01-24 13:46:11,235] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:11,237] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:11,237] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd5970db-7a57-4b70-bd75-5c740d1e6e1b/dqc_reference
[2024-01-24 13:46:12,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:12,514] [INFO] Task started: Prodigal
[2024-01-24 13:46:12,515] [INFO] Running command: gunzip -c /var/lib/cwl/stg16cab5b2-b63f-48eb-a40e-7e508d7da5d5/GCF_000308455.1_ASM30845v1_genomic.fna.gz | prodigal -d GCF_000308455.1_ASM30845v1_genomic.fna/cds.fna -a GCF_000308455.1_ASM30845v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:47,470] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:47,470] [INFO] Task started: HMMsearch
[2024-01-24 13:46:47,470] [INFO] Running command: hmmsearch --tblout GCF_000308455.1_ASM30845v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd5970db-7a57-4b70-bd75-5c740d1e6e1b/dqc_reference/reference_markers.hmm GCF_000308455.1_ASM30845v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:47,882] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:47,884] [INFO] Found 6/6 markers.
[2024-01-24 13:46:47,949] [INFO] Query marker FASTA was written to GCF_000308455.1_ASM30845v1_genomic.fna/markers.fasta
[2024-01-24 13:46:47,949] [INFO] Task started: Blastn
[2024-01-24 13:46:47,950] [INFO] Running command: blastn -query GCF_000308455.1_ASM30845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd5970db-7a57-4b70-bd75-5c740d1e6e1b/dqc_reference/reference_markers.fasta -out GCF_000308455.1_ASM30845v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:49,249] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:49,253] [INFO] Selected 7 target genomes.
[2024-01-24 13:46:49,253] [INFO] Target genome list was writen to GCF_000308455.1_ASM30845v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:49,260] [INFO] Task started: fastANI
[2024-01-24 13:46:49,260] [INFO] Running command: fastANI --query /var/lib/cwl/stg16cab5b2-b63f-48eb-a40e-7e508d7da5d5/GCF_000308455.1_ASM30845v1_genomic.fna.gz --refList GCF_000308455.1_ASM30845v1_genomic.fna/target_genomes.txt --output GCF_000308455.1_ASM30845v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:05,753] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:05,753] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd5970db-7a57-4b70-bd75-5c740d1e6e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:05,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd5970db-7a57-4b70-bd75-5c740d1e6e1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:05,761] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:47:05,761] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:47:05,761] [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 abscessus	strain=NBRC 100374	GCA_000308455.1	120957	120957	suspected-type	True	100.0	2697	2708	95	inconclusive
Nocardia abscessus	strain=FDAARGOS_1596	GCA_020731305.1	120957	120957	suspected-type	True	99.9994	2708	2708	95	inconclusive
Nocardia gipuzkoensis	strain=234509	GCA_013839485.1	2749991	2749991	type	True	95.9864	2205	2708	95	inconclusive
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	91.6811	2045	2708	95	below_threshold
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	90.9461	1907	2708	95	below_threshold
Nocardia gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	89.3054	1976	2708	95	below_threshold
Nocardia gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	89.2916	2009	2708	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:05,762] [INFO] DFAST Taxonomy check result was written to GCF_000308455.1_ASM30845v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:05,763] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:05,763] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:05,763] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd5970db-7a57-4b70-bd75-5c740d1e6e1b/dqc_reference/checkm_data
[2024-01-24 13:47:05,765] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:05,843] [INFO] Task started: CheckM
[2024-01-24 13:47:05,843] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000308455.1_ASM30845v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000308455.1_ASM30845v1_genomic.fna/checkm_input GCF_000308455.1_ASM30845v1_genomic.fna/checkm_result
[2024-01-24 13:48:39,004] [INFO] Task succeeded: CheckM
[2024-01-24 13:48:39,005] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.29%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:48:39,031] [INFO] ===== Completeness check finished =====
[2024-01-24 13:48:39,032] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:48:39,032] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000308455.1_ASM30845v1_genomic.fna/markers.fasta)
[2024-01-24 13:48:39,033] [INFO] Task started: Blastn
[2024-01-24 13:48:39,033] [INFO] Running command: blastn -query GCF_000308455.1_ASM30845v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd5970db-7a57-4b70-bd75-5c740d1e6e1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000308455.1_ASM30845v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:40,913] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:40,925] [INFO] Selected 9 target genomes.
[2024-01-24 13:48:40,926] [INFO] Target genome list was writen to GCF_000308455.1_ASM30845v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:48:40,935] [INFO] Task started: fastANI
[2024-01-24 13:48:40,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg16cab5b2-b63f-48eb-a40e-7e508d7da5d5/GCF_000308455.1_ASM30845v1_genomic.fna.gz --refList GCF_000308455.1_ASM30845v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000308455.1_ASM30845v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:48:59,471] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:59,488] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:48:59,488] [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_000308455.1	s__Nocardia abscessus	100.0	2697	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.07	95.78	0.84	0.83	5	conclusive
GCF_015477775.1	s__Nocardia abscessus_A	94.5978	2237	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013315795.1	s__Nocardia barduliensis	91.6687	2047	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308415.1	s__Nocardia asiatica	90.9445	1907	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829295.1	s__Nocardia sp009829295	89.4996	1905	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.64	99.39	0.96	0.94	4	-
GCF_001612765.1	s__Nocardia arthritidis	89.3845	1878	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_000308575.1	s__Nocardia exalbida	89.3272	1948	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_001612985.1	s__Nocardia gamkensis	89.3103	1976	2708	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_000308435.1	s__Nocardia araoensis	88.7581	1826	2708	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 13:48:59,490] [INFO] GTDB search result was written to GCF_000308455.1_ASM30845v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:48:59,491] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:48:59,495] [INFO] DFAST_QC result json was written to GCF_000308455.1_ASM30845v1_genomic.fna/dqc_result.json
[2024-01-24 13:48:59,495] [INFO] DFAST_QC completed!
[2024-01-24 13:48:59,495] [INFO] Total running time: 0h2m48s