[2024-01-24 13:46:40,666] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,668] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,668] [INFO] DQC Reference Directory: /var/lib/cwl/stg7f2691a5-610d-469d-9777-73ebcb8121ee/dqc_reference
[2024-01-24 13:46:41,939] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:41,940] [INFO] Task started: Prodigal
[2024-01-24 13:46:41,940] [INFO] Running command: gunzip -c /var/lib/cwl/stg6f0f1ebe-9ce2-41bb-8f29-a0c3383445c8/GCF_013315795.1_ASM1331579v1_genomic.fna.gz | prodigal -d GCF_013315795.1_ASM1331579v1_genomic.fna/cds.fna -a GCF_013315795.1_ASM1331579v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:47:16,012] [INFO] Task succeeded: Prodigal
[2024-01-24 13:47:16,013] [INFO] Task started: HMMsearch
[2024-01-24 13:47:16,013] [INFO] Running command: hmmsearch --tblout GCF_013315795.1_ASM1331579v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7f2691a5-610d-469d-9777-73ebcb8121ee/dqc_reference/reference_markers.hmm GCF_013315795.1_ASM1331579v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:47:16,361] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:47:16,362] [INFO] Found 6/6 markers.
[2024-01-24 13:47:16,429] [INFO] Query marker FASTA was written to GCF_013315795.1_ASM1331579v1_genomic.fna/markers.fasta
[2024-01-24 13:47:16,429] [INFO] Task started: Blastn
[2024-01-24 13:47:16,429] [INFO] Running command: blastn -query GCF_013315795.1_ASM1331579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f2691a5-610d-469d-9777-73ebcb8121ee/dqc_reference/reference_markers.fasta -out GCF_013315795.1_ASM1331579v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:17,673] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:17,676] [INFO] Selected 10 target genomes.
[2024-01-24 13:47:17,677] [INFO] Target genome list was writen to GCF_013315795.1_ASM1331579v1_genomic.fna/target_genomes.txt
[2024-01-24 13:47:17,687] [INFO] Task started: fastANI
[2024-01-24 13:47:17,687] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f0f1ebe-9ce2-41bb-8f29-a0c3383445c8/GCF_013315795.1_ASM1331579v1_genomic.fna.gz --refList GCF_013315795.1_ASM1331579v1_genomic.fna/target_genomes.txt --output GCF_013315795.1_ASM1331579v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:47:37,958] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:37,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7f2691a5-610d-469d-9777-73ebcb8121ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:47:37,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7f2691a5-610d-469d-9777-73ebcb8121ee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:47:37,968] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:47:37,968] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:47:37,968] [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 barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	100.0	2680	2691	95	conclusive
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	93.6781	1999	2691	95	below_threshold
Nocardia gipuzkoensis	strain=234509	GCA_013839485.1	2749991	2749991	type	True	91.6681	2047	2691	95	below_threshold
Nocardia abscessus	strain=NBRC 100374	GCA_000308455.1	120957	120957	suspected-type	True	91.6471	2024	2691	95	below_threshold
Nocardia abscessus	strain=FDAARGOS_1596	GCA_020731305.1	120957	120957	suspected-type	True	91.6316	2102	2691	95	below_threshold
Nocardia exalbida	strain=NBRC 100660	GCA_000308575.1	290231	290231	type	True	89.1587	1876	2691	95	below_threshold
Nocardia niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	88.6814	1846	2691	95	below_threshold
Nocardia araoensis	strain=NBRC 100135	GCA_000308435.1	228600	228600	type	True	88.6037	1752	2691	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	88.4334	1819	2691	95	below_threshold
Nocardia pneumoniae	strain=NBRC 100136	GCA_000308755.1	228601	228601	type	True	86.8365	1698	2691	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:47:37,969] [INFO] DFAST Taxonomy check result was written to GCF_013315795.1_ASM1331579v1_genomic.fna/tc_result.tsv
[2024-01-24 13:47:37,970] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:47:37,970] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:47:37,970] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7f2691a5-610d-469d-9777-73ebcb8121ee/dqc_reference/checkm_data
[2024-01-24 13:47:37,971] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:47:38,046] [INFO] Task started: CheckM
[2024-01-24 13:47:38,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013315795.1_ASM1331579v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013315795.1_ASM1331579v1_genomic.fna/checkm_input GCF_013315795.1_ASM1331579v1_genomic.fna/checkm_result
[2024-01-24 13:49:07,494] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:07,496] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.24%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2024-01-24 13:49:07,525] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:07,526] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:07,526] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013315795.1_ASM1331579v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:07,527] [INFO] Task started: Blastn
[2024-01-24 13:49:07,527] [INFO] Running command: blastn -query GCF_013315795.1_ASM1331579v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7f2691a5-610d-469d-9777-73ebcb8121ee/dqc_reference/reference_markers_gtdb.fasta -out GCF_013315795.1_ASM1331579v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:09,441] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:09,444] [INFO] Selected 13 target genomes.
[2024-01-24 13:49:09,445] [INFO] Target genome list was writen to GCF_013315795.1_ASM1331579v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:09,486] [INFO] Task started: fastANI
[2024-01-24 13:49:09,487] [INFO] Running command: fastANI --query /var/lib/cwl/stg6f0f1ebe-9ce2-41bb-8f29-a0c3383445c8/GCF_013315795.1_ASM1331579v1_genomic.fna.gz --refList GCF_013315795.1_ASM1331579v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013315795.1_ASM1331579v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:36,900] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:36,913] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:36,913] [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_013315795.1	s__Nocardia barduliensis	100.0	2680	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000308415.1	s__Nocardia asiatica	93.6869	1998	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477775.1	s__Nocardia abscessus_A	91.7848	2061	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308455.1	s__Nocardia abscessus	91.6433	2024	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.07	95.78	0.84	0.83	5	-
GCF_000308575.1	s__Nocardia exalbida	89.1559	1875	2691	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	89.1049	1919	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_009829295.1	s__Nocardia sp009829295	89.0796	1850	2691	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	89.0613	1801	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_000308435.1	s__Nocardia araoensis	88.6191	1750	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829325.1	s__Nocardia sp009829325	88.495	1879	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_001612785.1	s__Nocardia beijingensis	88.4198	1821	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_000308755.1	s__Nocardia pneumoniae	86.8104	1702	2691	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477605.1	s__Nocardia amamiensis_A	86.5328	1727	2691	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 13:49:36,915] [INFO] GTDB search result was written to GCF_013315795.1_ASM1331579v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:36,916] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:36,919] [INFO] DFAST_QC result json was written to GCF_013315795.1_ASM1331579v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:36,920] [INFO] DFAST_QC completed!
[2024-01-24 13:49:36,920] [INFO] Total running time: 0h2m56s