[2024-01-24 11:12:58,072] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:58,073] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:58,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg42b8fc43-42d3-4a54-8bb3-11dc71a214ab/dqc_reference
[2024-01-24 11:12:59,503] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:59,504] [INFO] Task started: Prodigal
[2024-01-24 11:12:59,504] [INFO] Running command: gunzip -c /var/lib/cwl/stg760a4d8b-9275-4201-8363-faebfa60160a/GCF_013181665.1_ASM1318166v1_genomic.fna.gz | prodigal -d GCF_013181665.1_ASM1318166v1_genomic.fna/cds.fna -a GCF_013181665.1_ASM1318166v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:13:31,893] [INFO] Task succeeded: Prodigal
[2024-01-24 11:13:31,893] [INFO] Task started: HMMsearch
[2024-01-24 11:13:31,894] [INFO] Running command: hmmsearch --tblout GCF_013181665.1_ASM1318166v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42b8fc43-42d3-4a54-8bb3-11dc71a214ab/dqc_reference/reference_markers.hmm GCF_013181665.1_ASM1318166v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:13:32,289] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:13:32,290] [INFO] Found 6/6 markers.
[2024-01-24 11:13:32,357] [INFO] Query marker FASTA was written to GCF_013181665.1_ASM1318166v1_genomic.fna/markers.fasta
[2024-01-24 11:13:32,358] [INFO] Task started: Blastn
[2024-01-24 11:13:32,358] [INFO] Running command: blastn -query GCF_013181665.1_ASM1318166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42b8fc43-42d3-4a54-8bb3-11dc71a214ab/dqc_reference/reference_markers.fasta -out GCF_013181665.1_ASM1318166v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:33,570] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:33,573] [INFO] Selected 6 target genomes.
[2024-01-24 11:13:33,573] [INFO] Target genome list was writen to GCF_013181665.1_ASM1318166v1_genomic.fna/target_genomes.txt
[2024-01-24 11:13:33,576] [INFO] Task started: fastANI
[2024-01-24 11:13:33,577] [INFO] Running command: fastANI --query /var/lib/cwl/stg760a4d8b-9275-4201-8363-faebfa60160a/GCF_013181665.1_ASM1318166v1_genomic.fna.gz --refList GCF_013181665.1_ASM1318166v1_genomic.fna/target_genomes.txt --output GCF_013181665.1_ASM1318166v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:13:46,670] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:46,671] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42b8fc43-42d3-4a54-8bb3-11dc71a214ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:13:46,671] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42b8fc43-42d3-4a54-8bb3-11dc71a214ab/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:13:46,677] [INFO] Found 6 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:13:46,678] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 11:13:46,678] [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 gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	100.0	2534	2537	95	inconclusive
Nocardia gamkensis	strain=DSM 44956	GCA_012396055.1	352869	352869	type	True	99.9982	2530	2537	95	inconclusive
Nocardia gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	99.9867	2473	2537	95	inconclusive
Nocardia exalbida	strain=NBRC 100660	GCA_000308575.1	290231	290231	type	True	96.6974	2104	2537	95	inconclusive
Nocardia arthritidis	strain=NBRC 100137	GCA_001612765.1	228602	228602	type	True	95.1109	1982	2537	95	inconclusive
Nocardia gipuzkoensis	strain=234509	GCA_013839485.1	2749991	2749991	type	True	89.5102	1994	2537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:13:46,679] [INFO] DFAST Taxonomy check result was written to GCF_013181665.1_ASM1318166v1_genomic.fna/tc_result.tsv
[2024-01-24 11:13:46,680] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:13:46,681] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:13:46,681] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42b8fc43-42d3-4a54-8bb3-11dc71a214ab/dqc_reference/checkm_data
[2024-01-24 11:13:46,682] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:13:46,756] [INFO] Task started: CheckM
[2024-01-24 11:13:46,757] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013181665.1_ASM1318166v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013181665.1_ASM1318166v1_genomic.fna/checkm_input GCF_013181665.1_ASM1318166v1_genomic.fna/checkm_result
[2024-01-24 11:15:12,306] [INFO] Task succeeded: CheckM
[2024-01-24 11:15:12,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 57.14%
--------------------------------------------------------------------------------
[2024-01-24 11:15:12,330] [INFO] ===== Completeness check finished =====
[2024-01-24 11:15:12,330] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:15:12,330] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013181665.1_ASM1318166v1_genomic.fna/markers.fasta)
[2024-01-24 11:15:12,331] [INFO] Task started: Blastn
[2024-01-24 11:15:12,331] [INFO] Running command: blastn -query GCF_013181665.1_ASM1318166v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42b8fc43-42d3-4a54-8bb3-11dc71a214ab/dqc_reference/reference_markers_gtdb.fasta -out GCF_013181665.1_ASM1318166v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:15:14,089] [INFO] Task succeeded: Blastn
[2024-01-24 11:15:14,094] [INFO] Selected 11 target genomes.
[2024-01-24 11:15:14,094] [INFO] Target genome list was writen to GCF_013181665.1_ASM1318166v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:15:14,102] [INFO] Task started: fastANI
[2024-01-24 11:15:14,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg760a4d8b-9275-4201-8363-faebfa60160a/GCF_013181665.1_ASM1318166v1_genomic.fna.gz --refList GCF_013181665.1_ASM1318166v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013181665.1_ASM1318166v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:15:38,013] [INFO] Task succeeded: fastANI
[2024-01-24 11:15:38,025] [INFO] Found 11 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 11:15:38,025] [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_001612985.1	s__Nocardia gamkensis	99.9867	2473	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	inconclusive
GCF_000308575.1	s__Nocardia exalbida	96.7053	2104	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_001612765.1	s__Nocardia arthritidis	95.12	1981	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	inconclusive
GCF_001613465.1	s__Nocardia niwae	89.9476	1974	2537	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	89.7196	1984	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_000308435.1	s__Nocardia araoensis	89.5835	1873	2537	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	89.5161	2069	2537	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	89.4209	1990	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.07	95.78	0.84	0.83	5	-
GCF_013315795.1	s__Nocardia barduliensis	89.1572	1933	2537	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	88.9255	1887	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.64	99.39	0.96	0.94	4	-
GCF_000308415.1	s__Nocardia asiatica	88.895	1786	2537	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 11:15:38,026] [INFO] GTDB search result was written to GCF_013181665.1_ASM1318166v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:15:38,027] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:15:38,030] [INFO] DFAST_QC result json was written to GCF_013181665.1_ASM1318166v1_genomic.fna/dqc_result.json
[2024-01-24 11:15:38,030] [INFO] DFAST_QC completed!
[2024-01-24 11:15:38,030] [INFO] Total running time: 0h2m40s