[2024-01-24 14:47:48,963] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:47:48,965] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:47:48,965] [INFO] DQC Reference Directory: /var/lib/cwl/stg43d20393-c021-481e-ad69-7aa1e85ed932/dqc_reference
[2024-01-24 14:47:50,544] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:47:50,545] [INFO] Task started: Prodigal
[2024-01-24 14:47:50,545] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe153e7f-278f-449e-8fa0-3314dec63c4b/GCF_001613145.1_ASM161314v1_genomic.fna.gz | prodigal -d GCF_001613145.1_ASM161314v1_genomic.fna/cds.fna -a GCF_001613145.1_ASM161314v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:48:38,224] [INFO] Task succeeded: Prodigal
[2024-01-24 14:48:38,225] [INFO] Task started: HMMsearch
[2024-01-24 14:48:38,225] [INFO] Running command: hmmsearch --tblout GCF_001613145.1_ASM161314v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg43d20393-c021-481e-ad69-7aa1e85ed932/dqc_reference/reference_markers.hmm GCF_001613145.1_ASM161314v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:48:38,624] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:48:38,625] [INFO] Found 6/6 markers.
[2024-01-24 14:48:38,691] [INFO] Query marker FASTA was written to GCF_001613145.1_ASM161314v1_genomic.fna/markers.fasta
[2024-01-24 14:48:38,692] [INFO] Task started: Blastn
[2024-01-24 14:48:38,692] [INFO] Running command: blastn -query GCF_001613145.1_ASM161314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d20393-c021-481e-ad69-7aa1e85ed932/dqc_reference/reference_markers.fasta -out GCF_001613145.1_ASM161314v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:40,000] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:40,004] [INFO] Selected 16 target genomes.
[2024-01-24 14:48:40,004] [INFO] Target genome list was writen to GCF_001613145.1_ASM161314v1_genomic.fna/target_genomes.txt
[2024-01-24 14:48:40,015] [INFO] Task started: fastANI
[2024-01-24 14:48:40,015] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe153e7f-278f-449e-8fa0-3314dec63c4b/GCF_001613145.1_ASM161314v1_genomic.fna.gz --refList GCF_001613145.1_ASM161314v1_genomic.fna/target_genomes.txt --output GCF_001613145.1_ASM161314v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:49:14,388] [INFO] Task succeeded: fastANI
[2024-01-24 14:49:14,389] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg43d20393-c021-481e-ad69-7aa1e85ed932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:49:14,389] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg43d20393-c021-481e-ad69-7aa1e85ed932/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:49:14,409] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:49:14,409] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:49:14,409] [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 jejuensis	strain=NBRC 103114	GCA_001613145.1	328049	328049	type	True	100.0	2831	2836	95	conclusive
Nocardia seriolae	strain=NBRC 15557	GCA_007990715.1	37332	37332	type	True	82.7481	1464	2836	95	below_threshold
Nocardia yunnanensis	strain=CFH S0054	GCA_003626895.1	2382165	2382165	type	True	82.6792	1602	2836	95	below_threshold
Nocardia concava	strain=NBRC 100430	GCA_000308815.1	257281	257281	type	True	82.6634	1606	2836	95	below_threshold
Nocardia terrae	strain=ET3-3	GCA_009760405.1	2675851	2675851	type	True	82.6392	1616	2836	95	below_threshold
Nocardia yamanashiensis	strain=NBRC 100130	GCA_001613325.1	209247	209247	type	True	82.6201	1695	2836	95	below_threshold
Nocardia niigatensis	strain=NBRC 100131	GCA_000308655.1	209249	209249	type	True	82.5936	1546	2836	95	below_threshold
Nocardia acidivorans	strain=NBRC 108247	GCA_001625085.1	404580	404580	type	True	82.5637	1601	2836	95	below_threshold
Nocardia huaxiensis	strain=WCH-YHL-001	GCA_013744875.1	2755382	2755382	type	True	82.4846	1560	2836	95	below_threshold
Nocardia inohanensis	strain=NBRC 100128	GCA_001612945.1	209246	209246	type	True	82.4598	1649	2836	95	below_threshold
Nocardia acididurans	strain=LPG 2	GCA_016741815.1	2802282	2802282	type	True	82.4534	1611	2836	95	below_threshold
Nocardia crassostreae	strain=NBRC 100342	GCA_001613405.1	53428	53428	type	True	82.379	1480	2836	95	below_threshold
Nocardia otitidiscaviarum	strain=NCTC1934	GCA_900454305.1	1823	1823	type	True	81.6993	1396	2836	95	below_threshold
Nocardia otitidiscaviarum	strain=NBRC 14405	GCA_000308635.1	1823	1823	type	True	81.6871	1381	2836	95	below_threshold
Nocardia uniformis	strain=JCM 3224	GCA_013004475.1	53432	53432	type	True	80.9446	1363	2836	95	below_threshold
Nocardia uniformis	strain=NBRC 13702	GCA_001613345.1	53432	53432	type	True	80.8974	1351	2836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:49:14,411] [INFO] DFAST Taxonomy check result was written to GCF_001613145.1_ASM161314v1_genomic.fna/tc_result.tsv
[2024-01-24 14:49:14,412] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:49:14,412] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:49:14,412] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg43d20393-c021-481e-ad69-7aa1e85ed932/dqc_reference/checkm_data
[2024-01-24 14:49:14,413] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:49:14,491] [INFO] Task started: CheckM
[2024-01-24 14:49:14,491] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613145.1_ASM161314v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613145.1_ASM161314v1_genomic.fna/checkm_input GCF_001613145.1_ASM161314v1_genomic.fna/checkm_result
[2024-01-24 14:51:20,074] [INFO] Task succeeded: CheckM
[2024-01-24 14:51:20,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:51:20,109] [INFO] ===== Completeness check finished =====
[2024-01-24 14:51:20,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:51:20,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613145.1_ASM161314v1_genomic.fna/markers.fasta)
[2024-01-24 14:51:20,110] [INFO] Task started: Blastn
[2024-01-24 14:51:20,111] [INFO] Running command: blastn -query GCF_001613145.1_ASM161314v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg43d20393-c021-481e-ad69-7aa1e85ed932/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613145.1_ASM161314v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:51:22,182] [INFO] Task succeeded: Blastn
[2024-01-24 14:51:22,186] [INFO] Selected 17 target genomes.
[2024-01-24 14:51:22,186] [INFO] Target genome list was writen to GCF_001613145.1_ASM161314v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:51:22,205] [INFO] Task started: fastANI
[2024-01-24 14:51:22,206] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe153e7f-278f-449e-8fa0-3314dec63c4b/GCF_001613145.1_ASM161314v1_genomic.fna.gz --refList GCF_001613145.1_ASM161314v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613145.1_ASM161314v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:51:58,522] [INFO] Task succeeded: fastANI
[2024-01-24 14:51:58,542] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:51:58,542] [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_001613145.1	s__Nocardia jejuensis	100.0	2831	2836	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_018362975.1	s__Nocardia tengchongensis	82.7736	1559	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990715.1	s__Nocardia seriolae	82.7564	1463	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.94	99.87	0.97	0.93	20	-
GCF_000308815.1	s__Nocardia concava	82.6936	1601	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626895.1	s__Nocardia yunnanensis	82.6766	1603	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613325.1	s__Nocardia yamanashiensis	82.6153	1696	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760405.1	s__Nocardia terrae	82.6116	1620	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308655.1	s__Nocardia niigatensis	82.6098	1541	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001625085.1	s__Nocardia acidivorans	82.5602	1601	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013744875.1	s__Nocardia sp013744875	82.4876	1559	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612945.1	s__Nocardia inohanensis	82.4586	1649	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741815.1	s__Nocardia sp016741815	82.4485	1613	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613405.1	s__Nocardia crassostreae	82.3541	1484	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009649815.1	s__Nocardia sp009649815	82.2149	1597	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308635.1	s__Nocardia otitidiscaviarum	81.7044	1377	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.88	97.41	0.94	0.92	8	-
GCF_001613345.1	s__Nocardia uniformis	80.8883	1354	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000284035.1	s__Nocardia cyriacigeorgica_B	80.0295	992	2836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.41	98.27	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:51:58,544] [INFO] GTDB search result was written to GCF_001613145.1_ASM161314v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:51:58,545] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:51:58,549] [INFO] DFAST_QC result json was written to GCF_001613145.1_ASM161314v1_genomic.fna/dqc_result.json
[2024-01-24 14:51:58,550] [INFO] DFAST_QC completed!
[2024-01-24 14:51:58,550] [INFO] Total running time: 0h4m10s