[2024-01-25 18:44:50,630] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:44:50,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:44:50,632] [INFO] DQC Reference Directory: /var/lib/cwl/stga5c95a2d-a9ea-4632-acbe-2fb7384b2f65/dqc_reference
[2024-01-25 18:44:51,782] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:44:51,783] [INFO] Task started: Prodigal
[2024-01-25 18:44:51,783] [INFO] Running command: gunzip -c /var/lib/cwl/stg4678f838-db76-4bfd-b189-d01c553ba637/GCF_014191425.1_ASM1419142v1_genomic.fna.gz | prodigal -d GCF_014191425.1_ASM1419142v1_genomic.fna/cds.fna -a GCF_014191425.1_ASM1419142v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:44:58,706] [INFO] Task succeeded: Prodigal
[2024-01-25 18:44:58,706] [INFO] Task started: HMMsearch
[2024-01-25 18:44:58,706] [INFO] Running command: hmmsearch --tblout GCF_014191425.1_ASM1419142v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga5c95a2d-a9ea-4632-acbe-2fb7384b2f65/dqc_reference/reference_markers.hmm GCF_014191425.1_ASM1419142v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:44:58,886] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:44:58,887] [INFO] Found 6/6 markers.
[2024-01-25 18:44:58,910] [INFO] Query marker FASTA was written to GCF_014191425.1_ASM1419142v1_genomic.fna/markers.fasta
[2024-01-25 18:44:58,910] [INFO] Task started: Blastn
[2024-01-25 18:44:58,910] [INFO] Running command: blastn -query GCF_014191425.1_ASM1419142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c95a2d-a9ea-4632-acbe-2fb7384b2f65/dqc_reference/reference_markers.fasta -out GCF_014191425.1_ASM1419142v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:44:59,961] [INFO] Task succeeded: Blastn
[2024-01-25 18:44:59,964] [INFO] Selected 22 target genomes.
[2024-01-25 18:44:59,964] [INFO] Target genome list was writen to GCF_014191425.1_ASM1419142v1_genomic.fna/target_genomes.txt
[2024-01-25 18:44:59,979] [INFO] Task started: fastANI
[2024-01-25 18:44:59,980] [INFO] Running command: fastANI --query /var/lib/cwl/stg4678f838-db76-4bfd-b189-d01c553ba637/GCF_014191425.1_ASM1419142v1_genomic.fna.gz --refList GCF_014191425.1_ASM1419142v1_genomic.fna/target_genomes.txt --output GCF_014191425.1_ASM1419142v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:45:12,995] [INFO] Task succeeded: fastANI
[2024-01-25 18:45:12,996] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga5c95a2d-a9ea-4632-acbe-2fb7384b2f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:45:12,996] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga5c95a2d-a9ea-4632-acbe-2fb7384b2f65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:45:13,009] [INFO] Found 22 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:45:13,009] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:45:13,009] [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
Brachybacterium aquaticum	strain=DSM 28796	GCA_014204755.1	1432564	1432564	type	True	79.7333	370	858	95	below_threshold
Brachybacterium squillarum	strain=M-6-3	GCA_000225825.2	661979	661979	type	True	79.5562	380	858	95	below_threshold
Brachybacterium massiliense	strain=mt5	GCA_900184245.1	1755098	1755098	type	True	79.5474	350	858	95	below_threshold
Brachybacterium muris	strain=DSM 15460	GCA_016907455.1	219301	219301	type	True	79.5136	342	858	95	below_threshold
Brachybacterium epidermidis	strain=Marseille-Q2903	GCA_015209585.1	2781983	2781983	type	True	79.4828	332	858	95	below_threshold
Dermabacter jinjuensis	strain=FDAARGOS_1555	GCA_020736445.1	1667168	1667168	type	True	79.462	183	858	95	below_threshold
Dermabacter jinjuensis	strain=32T	GCA_002443115.1	1667168	1667168	type	True	79.4386	192	858	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003355475.1	556288	556288	type	True	79.0976	378	858	95	below_threshold
Brachybacterium kimchii	strain=CBA3104	GCA_023373525.1	2942909	2942909	type	True	79.0179	335	858	95	below_threshold
Brachybacterium halotolerans subsp. kimchii	strain=CBA3105	GCA_020792675.1	2887346	2795215	type	True	79.0148	352	858	95	below_threshold
Brachybacterium saurashtrense	strain=DSM 23186	GCA_003994295.1	556288	556288	type	True	78.9924	373	858	95	below_threshold
Brachybacterium nesterenkovii	strain=CIP104813	GCA_900163655.1	47847	47847	type	True	78.9345	334	858	95	below_threshold
Brachybacterium ginsengisoli	strain=DCY80	GCA_002407065.1	1331682	1331682	type	True	78.927	342	858	95	below_threshold
Brachybacterium halotolerans	strain=MASK1Z-5	GCA_016623465.1	2795215	2795215	type	True	78.9171	330	858	95	below_threshold
Brachybacterium subflavum	strain=CFH 10395	GCA_009299795.1	2585206	2585206	type	True	78.8849	337	858	95	below_threshold
Brachybacterium sacelli	strain=DSM 14566	GCA_017876545.1	173364	173364	type	True	78.6893	337	858	95	below_threshold
Oceanitalea stevensii	strain=Sa1BUA1	GCA_014837105.1	2763072	2763072	type	True	77.3005	180	858	95	below_threshold
Microbacterium oryzae	strain=MB-10	GCA_009735645.1	743009	743009	type	True	77.0283	148	858	95	below_threshold
Bifidobacterium aesculapii	strain=DSM 26737	GCA_001417815.1	1329411	1329411	type	True	76.9715	91	858	95	below_threshold
Occultella glacieicola	strain=T3246-1	GCA_004353825.1	2518684	2518684	type	True	76.8068	166	858	95	below_threshold
Agrococcus jejuensis	strain=DSM 22002	GCA_900099705.1	399736	399736	type	True	76.6359	168	858	95	below_threshold
Microbacterium nanhaiense	strain=CGMCC 4.7181	GCA_014646015.1	1301026	1301026	type	True	76.2144	126	858	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:45:13,010] [INFO] DFAST Taxonomy check result was written to GCF_014191425.1_ASM1419142v1_genomic.fna/tc_result.tsv
[2024-01-25 18:45:13,011] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:45:13,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:45:13,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga5c95a2d-a9ea-4632-acbe-2fb7384b2f65/dqc_reference/checkm_data
[2024-01-25 18:45:13,012] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:45:13,039] [INFO] Task started: CheckM
[2024-01-25 18:45:13,039] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014191425.1_ASM1419142v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014191425.1_ASM1419142v1_genomic.fna/checkm_input GCF_014191425.1_ASM1419142v1_genomic.fna/checkm_result
[2024-01-25 18:45:48,064] [INFO] Task succeeded: CheckM
[2024-01-25 18:45:48,066] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:45:48,081] [INFO] ===== Completeness check finished =====
[2024-01-25 18:45:48,081] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:45:48,081] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014191425.1_ASM1419142v1_genomic.fna/markers.fasta)
[2024-01-25 18:45:48,082] [INFO] Task started: Blastn
[2024-01-25 18:45:48,082] [INFO] Running command: blastn -query GCF_014191425.1_ASM1419142v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga5c95a2d-a9ea-4632-acbe-2fb7384b2f65/dqc_reference/reference_markers_gtdb.fasta -out GCF_014191425.1_ASM1419142v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:45:49,967] [INFO] Task succeeded: Blastn
[2024-01-25 18:45:49,976] [INFO] Selected 19 target genomes.
[2024-01-25 18:45:49,976] [INFO] Target genome list was writen to GCF_014191425.1_ASM1419142v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:45:50,005] [INFO] Task started: fastANI
[2024-01-25 18:45:50,005] [INFO] Running command: fastANI --query /var/lib/cwl/stg4678f838-db76-4bfd-b189-d01c553ba637/GCF_014191425.1_ASM1419142v1_genomic.fna.gz --refList GCF_014191425.1_ASM1419142v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014191425.1_ASM1419142v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:46:01,473] [INFO] Task succeeded: fastANI
[2024-01-25 18:46:01,484] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:46:01,485] [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_014191425.1	s__Helcobacillus massiliensis	100.0	850	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Helcobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014204755.1	s__Brachybacterium aquaticum	79.7396	369	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000225825.1	s__Brachybacterium squillarum	79.6545	377	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002871795.1	s__Brachybacterium sp002871795	79.6286	345	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005490785.1	s__Brachybacterium sp005490785	79.6194	332	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016907455.1	s__Brachybacterium muris	79.4902	343	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	97.23	96.65	0.88	0.85	3	-
GCF_900184245.1	s__Brachybacterium massiliense	79.4638	348	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003355475.1	s__Brachybacterium saurashtrense	79.1949	383	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000576425.1	s__Brachybacterium phenoliresistens	79.0695	366	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003711805.1	s__Brachybacterium intestinipullorum	79.0186	358	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	99.17	99.17	0.95	0.95	2	-
GCF_900163655.1	s__Brachybacterium nesterenkovii	78.9512	334	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002407065.1	s__Brachybacterium ginsengisoli	78.9456	340	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016623465.1	s__Brachybacterium halotolerans	78.9303	329	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009299795.1	s__Brachybacterium subflavum	78.8598	339	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001403775.1	s__Dermabacter massiliensis_A	78.5836	186	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Dermabacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019118275.1	s__Brachybacterium merdavium	78.3261	272	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermabacteraceae;g__Brachybacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417815.1	s__Bifidobacterium aesculapii	76.9997	90	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Bifidobacteriaceae;g__Bifidobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646015.1	s__Microbacterium nanhaiense	76.2144	126	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019117025.1	s__Microbacterium stercoravium	76.1153	94	858	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Microbacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:46:01,486] [INFO] GTDB search result was written to GCF_014191425.1_ASM1419142v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:46:01,487] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:46:01,491] [INFO] DFAST_QC result json was written to GCF_014191425.1_ASM1419142v1_genomic.fna/dqc_result.json
[2024-01-25 18:46:01,491] [INFO] DFAST_QC completed!
[2024-01-25 18:46:01,491] [INFO] Total running time: 0h1m11s