[2024-01-25 19:11:20,718] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:20,719] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:20,719] [INFO] DQC Reference Directory: /var/lib/cwl/stgc811ecf8-6a3c-4209-9b61-17fad1846345/dqc_reference
[2024-01-25 19:11:21,831] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:21,832] [INFO] Task started: Prodigal
[2024-01-25 19:11:21,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgcad1300e-6e85-4f6d-a463-8ee6af7f8122/GCF_001315085.1_ASM131508v1_genomic.fna.gz | prodigal -d GCF_001315085.1_ASM131508v1_genomic.fna/cds.fna -a GCF_001315085.1_ASM131508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:29,437] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:29,438] [INFO] Task started: HMMsearch
[2024-01-25 19:11:29,438] [INFO] Running command: hmmsearch --tblout GCF_001315085.1_ASM131508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc811ecf8-6a3c-4209-9b61-17fad1846345/dqc_reference/reference_markers.hmm GCF_001315085.1_ASM131508v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:29,726] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:29,727] [INFO] Found 6/6 markers.
[2024-01-25 19:11:29,768] [INFO] Query marker FASTA was written to GCF_001315085.1_ASM131508v1_genomic.fna/markers.fasta
[2024-01-25 19:11:29,768] [INFO] Task started: Blastn
[2024-01-25 19:11:29,768] [INFO] Running command: blastn -query GCF_001315085.1_ASM131508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc811ecf8-6a3c-4209-9b61-17fad1846345/dqc_reference/reference_markers.fasta -out GCF_001315085.1_ASM131508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:30,327] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:30,331] [INFO] Selected 16 target genomes.
[2024-01-25 19:11:30,332] [INFO] Target genome list was writen to GCF_001315085.1_ASM131508v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:30,339] [INFO] Task started: fastANI
[2024-01-25 19:11:30,339] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad1300e-6e85-4f6d-a463-8ee6af7f8122/GCF_001315085.1_ASM131508v1_genomic.fna.gz --refList GCF_001315085.1_ASM131508v1_genomic.fna/target_genomes.txt --output GCF_001315085.1_ASM131508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:42,112] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:42,112] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc811ecf8-6a3c-4209-9b61-17fad1846345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:42,113] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc811ecf8-6a3c-4209-9b61-17fad1846345/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:42,121] [INFO] Found 12 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:11:42,122] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:42,122] [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
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	100.0	1504	1509	95	conclusive
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	100.0	1504	1509	95	conclusive
Alkalihalobacillus okhensis	strain=Kh10-101	GCA_000787375.1	333138	333138	type	True	80.1412	440	1509	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_001315065.1	127886	127886	type	True	79.764	204	1509	95	below_threshold
Alkalihalobacillus hemicellulosilyticus	strain=JCM 9152	GCA_000513115.1	127886	127886	type	True	79.7538	204	1509	95	below_threshold
Alkalihalobacillus krulwichiae	strain=AM31D	GCA_002109385.1	199441	199441	type	True	79.6973	473	1509	95	below_threshold
Alkalihalobacillus krulwichiae	strain=NBRC 102362	GCA_001591945.1	199441	199441	type	True	79.5916	464	1509	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.9916	249	1509	95	below_threshold
Fictibacillus norfolkensis	strain=Sa2CUA10	GCA_014836645.1	2762233	2762233	type	True	76.8702	51	1509	95	below_threshold
Alkalihalobacillus bogoriensis	strain=ATCC BAA-922	GCA_000621445.1	246272	246272	type	True	76.753	168	1509	95	below_threshold
Neobacillus kokaensis	strain=LOB 377	GCA_014656545.1	2759023	2759023	type	True	76.4927	53	1509	95	below_threshold
Pseudalkalibacillus decolorationis	strain=DSM 14890	GCA_024609785.1	163879	163879	type	True	76.455	55	1509	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:42,123] [INFO] DFAST Taxonomy check result was written to GCF_001315085.1_ASM131508v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:42,124] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:42,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:42,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc811ecf8-6a3c-4209-9b61-17fad1846345/dqc_reference/checkm_data
[2024-01-25 19:11:42,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:42,171] [INFO] Task started: CheckM
[2024-01-25 19:11:42,172] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001315085.1_ASM131508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001315085.1_ASM131508v1_genomic.fna/checkm_input GCF_001315085.1_ASM131508v1_genomic.fna/checkm_result
[2024-01-25 19:12:09,141] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:09,142] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:09,160] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:09,160] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:09,161] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001315085.1_ASM131508v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:09,162] [INFO] Task started: Blastn
[2024-01-25 19:12:09,162] [INFO] Running command: blastn -query GCF_001315085.1_ASM131508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc811ecf8-6a3c-4209-9b61-17fad1846345/dqc_reference/reference_markers_gtdb.fasta -out GCF_001315085.1_ASM131508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:09,917] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:09,921] [INFO] Selected 17 target genomes.
[2024-01-25 19:12:09,921] [INFO] Target genome list was writen to GCF_001315085.1_ASM131508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:09,929] [INFO] Task started: fastANI
[2024-01-25 19:12:09,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgcad1300e-6e85-4f6d-a463-8ee6af7f8122/GCF_001315085.1_ASM131508v1_genomic.fna.gz --refList GCF_001315085.1_ASM131508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001315085.1_ASM131508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:12:22,759] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:22,769] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:12:22,769] [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_000513135.1	s__Bacillus_L akibai	100.0	1504	1509	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	conclusive
GCF_000787375.1	s__Bacillus_L okhensis	80.1213	442	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000513095.1	s__Bacillus_L wakoensis	79.8805	424	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000513115.1	s__Bacillus_L hemicellulosilyticus	79.7787	203	1509	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_000005825.2	s__Bacillus_S pseudofirmus	79.7439	192	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.9507	97.22	97.22	0.89	0.89	2	-
GCF_002109385.1	s__Bacillus_L krulwichiae	79.6864	474	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	99.99	99.99	1.00	1.00	2	-
GCF_007830185.1	s__Bacillus_L nanhaiisediminis	78.4802	240	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017939705.1	s__Bacillus_L sp017939705	78.0337	246	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_L	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000474275.2	s__Bacillus_S marmarensis	77.8947	170	1509	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_002797325.1	s__Bacillus_S sp002797325	77.8549	165	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_S	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001590785.1	s__Alkalihalobacillus trypoxylicola	77.3883	119	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus	95.0	98.48	96.97	0.95	0.90	3	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	77.0566	127	1509	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_001866005.1	s__Anaerobacillus alkalilacustris	76.8151	95	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000621445.1	s__Bacillus_AO bogoriensis	76.7654	168	1509	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_002200015.1	s__Bacillus_A cereus_AZ	76.4078	70	1509	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	96.9563	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:12:22,771] [INFO] GTDB search result was written to GCF_001315085.1_ASM131508v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:12:22,771] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:12:22,778] [INFO] DFAST_QC result json was written to GCF_001315085.1_ASM131508v1_genomic.fna/dqc_result.json
[2024-01-25 19:12:22,778] [INFO] DFAST_QC completed!
[2024-01-25 19:12:22,779] [INFO] Total running time: 0h1m2s