[2024-01-24 14:07:00,220] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:00,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:00,222] [INFO] DQC Reference Directory: /var/lib/cwl/stgf658e680-82b2-4f38-b765-3b92ccbfcc97/dqc_reference
[2024-01-24 14:07:01,548] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:01,549] [INFO] Task started: Prodigal
[2024-01-24 14:07:01,549] [INFO] Running command: gunzip -c /var/lib/cwl/stg33ea59d8-3b81-4246-b46a-dacb343b674d/GCF_019039105.1_ASM1903910v1_genomic.fna.gz | prodigal -d GCF_019039105.1_ASM1903910v1_genomic.fna/cds.fna -a GCF_019039105.1_ASM1903910v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:11,067] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:11,067] [INFO] Task started: HMMsearch
[2024-01-24 14:07:11,067] [INFO] Running command: hmmsearch --tblout GCF_019039105.1_ASM1903910v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf658e680-82b2-4f38-b765-3b92ccbfcc97/dqc_reference/reference_markers.hmm GCF_019039105.1_ASM1903910v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:11,316] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:11,317] [INFO] Found 6/6 markers.
[2024-01-24 14:07:11,357] [INFO] Query marker FASTA was written to GCF_019039105.1_ASM1903910v1_genomic.fna/markers.fasta
[2024-01-24 14:07:11,357] [INFO] Task started: Blastn
[2024-01-24 14:07:11,357] [INFO] Running command: blastn -query GCF_019039105.1_ASM1903910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf658e680-82b2-4f38-b765-3b92ccbfcc97/dqc_reference/reference_markers.fasta -out GCF_019039105.1_ASM1903910v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:11,965] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:11,969] [INFO] Selected 22 target genomes.
[2024-01-24 14:07:11,969] [INFO] Target genome list was writen to GCF_019039105.1_ASM1903910v1_genomic.fna/target_genomes.txt
[2024-01-24 14:07:11,980] [INFO] Task started: fastANI
[2024-01-24 14:07:11,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg33ea59d8-3b81-4246-b46a-dacb343b674d/GCF_019039105.1_ASM1903910v1_genomic.fna.gz --refList GCF_019039105.1_ASM1903910v1_genomic.fna/target_genomes.txt --output GCF_019039105.1_ASM1903910v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:26,886] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:26,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf658e680-82b2-4f38-b765-3b92ccbfcc97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:26,886] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf658e680-82b2-4f38-b765-3b92ccbfcc97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:26,899] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:07:26,899] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:26,899] [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
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	100.0	1364	1366	95	conclusive
Alkalihalobacterium elongatum	strain=MEB199	GCA_019024285.1	2675466	2675466	type	True	77.3063	132	1366	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	77.1422	159	1366	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_000513115.1	127886	127886	type	True	76.9954	87	1366	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_001315065.1	127886	127886	type	True	76.9733	86	1366	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.9045	112	1366	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	76.9041	141	1366	95	below_threshold
Bacillus anthracis	strain=Vollum	GCA_022221345.1	1392	1392	type	True	76.8074	61	1366	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	76.7356	92	1366	95	below_threshold
Alkalihalobacillus alcalophilus	strain=AV1934	GCA_000292245.2	1445	1445	type	True	76.6888	83	1366	95	below_threshold
Alkalihalobacillus alcalophilus	strain=CGMCC 1.3604	GCA_004802515.1	1445	1445	type	True	76.5962	75	1366	95	below_threshold
Alteribacter populi	strain=FJAT-45347	GCA_002352765.2	2011011	2011011	type	True	76.5427	65	1366	95	below_threshold
Cytobacillus solani	strain=FJAT-18043	GCA_001420595.1	1637975	1637975	type	True	76.4613	51	1366	95	below_threshold
Bacillus solimangrovi	strain=GH2-4	GCA_001742425.1	1305675	1305675	type	True	76.4471	57	1366	95	below_threshold
Gottfriedia solisilvae	strain=CGMCC 1.14993	GCA_014640495.1	1516104	1516104	type	True	76.3355	51	1366	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:26,901] [INFO] DFAST Taxonomy check result was written to GCF_019039105.1_ASM1903910v1_genomic.fna/tc_result.tsv
[2024-01-24 14:07:26,902] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:26,902] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:26,902] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf658e680-82b2-4f38-b765-3b92ccbfcc97/dqc_reference/checkm_data
[2024-01-24 14:07:26,904] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:26,946] [INFO] Task started: CheckM
[2024-01-24 14:07:26,947] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019039105.1_ASM1903910v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019039105.1_ASM1903910v1_genomic.fna/checkm_input GCF_019039105.1_ASM1903910v1_genomic.fna/checkm_result
[2024-01-24 14:08:00,631] [INFO] Task succeeded: CheckM
[2024-01-24 14:08:00,632] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 5.93%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:08:00,653] [INFO] ===== Completeness check finished =====
[2024-01-24 14:08:00,653] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:08:00,653] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019039105.1_ASM1903910v1_genomic.fna/markers.fasta)
[2024-01-24 14:08:00,654] [INFO] Task started: Blastn
[2024-01-24 14:08:00,654] [INFO] Running command: blastn -query GCF_019039105.1_ASM1903910v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf658e680-82b2-4f38-b765-3b92ccbfcc97/dqc_reference/reference_markers_gtdb.fasta -out GCF_019039105.1_ASM1903910v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:08:01,450] [INFO] Task succeeded: Blastn
[2024-01-24 14:08:01,454] [INFO] Selected 26 target genomes.
[2024-01-24 14:08:01,454] [INFO] Target genome list was writen to GCF_019039105.1_ASM1903910v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:08:01,483] [INFO] Task started: fastANI
[2024-01-24 14:08:01,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg33ea59d8-3b81-4246-b46a-dacb343b674d/GCF_019039105.1_ASM1903910v1_genomic.fna.gz --refList GCF_019039105.1_ASM1903910v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019039105.1_ASM1903910v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:08:21,406] [INFO] Task succeeded: fastANI
[2024-01-24 14:08:21,422] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:08:21,422] [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_019039105.1	s__Desertibacillus haloalkaliphilus	100.0	1364	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__KJ1-10-99;g__Desertibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_002335805.1	s__FJAT-45350 sp002335805	77.4213	144	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__FJAT-45350	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019024285.1	s__Bacillus_BH sp019024285	77.3265	131	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156385.1	s__45385 sp002156385	77.1152	120	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__45385	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	77.1094	161	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	97.46	97.46	0.83	0.83	2	-
GCF_900197585.1	s__Bacillus_H sp900197585	77.0969	53	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021305.1	s__Bacillus_A thuringiensis_S	77.0082	63	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.4134	98.69	97.04	0.88	0.75	230	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	76.9954	87	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	76.9208	140	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_AO	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	76.9045	112	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	N/A	N/A	N/A	N/A	1	-
GCF_001439915.1	s__Fredinandcohnia humi	76.8162	58	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_L;g__Fredinandcohnia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	76.7962	83	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017745675.1	s__Bacillus_BH sp017745675	76.7918	161	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_F;g__Bacillus_BH	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001455345.1	s__Bacillus_A thuringiensis_N	76.7575	60	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.23	95.30	0.91	0.84	24	-
GCF_000292245.2	s__Alkalihalobacillus alcalophilus	76.6847	85	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	99.90	99.82	0.98	0.98	3	-
GCF_002352765.1	s__Alteribacter populi	76.5504	66	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Salisediminibacteriaceae;g__Alteribacter	95.0	99.66	99.66	0.95	0.95	2	-
GCF_001742425.1	s__Bacillus_AV solimangrovi	76.4471	57	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_D;f__Bacillaceae_N;g__Bacillus_AV	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156875.1	s__Robertmurraya dakarensis	76.441	67	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Robertmurraya	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001883995.1	s__Bacillus_A paranthracis	76.2698	60	1366	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.3658	97.40	95.70	0.86	0.80	231	-
--------------------------------------------------------------------------------
[2024-01-24 14:08:21,424] [INFO] GTDB search result was written to GCF_019039105.1_ASM1903910v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:08:21,425] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:08:21,429] [INFO] DFAST_QC result json was written to GCF_019039105.1_ASM1903910v1_genomic.fna/dqc_result.json
[2024-01-24 14:08:21,430] [INFO] DFAST_QC completed!
[2024-01-24 14:08:21,430] [INFO] Total running time: 0h1m21s