[2024-01-24 14:19:02,268] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:02,271] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:02,271] [INFO] DQC Reference Directory: /var/lib/cwl/stg1afa81e7-fcd1-4851-bd54-782ca3812039/dqc_reference
[2024-01-24 14:19:03,496] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:03,497] [INFO] Task started: Prodigal
[2024-01-24 14:19:03,497] [INFO] Running command: gunzip -c /var/lib/cwl/stg97307b1e-4c96-4e05-ae4d-df25a47a5078/GCF_023703085.1_ASM2370308v1_genomic.fna.gz | prodigal -d GCF_023703085.1_ASM2370308v1_genomic.fna/cds.fna -a GCF_023703085.1_ASM2370308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:12,908] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:12,908] [INFO] Task started: HMMsearch
[2024-01-24 14:19:12,909] [INFO] Running command: hmmsearch --tblout GCF_023703085.1_ASM2370308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1afa81e7-fcd1-4851-bd54-782ca3812039/dqc_reference/reference_markers.hmm GCF_023703085.1_ASM2370308v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:13,199] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:13,201] [INFO] Found 6/6 markers.
[2024-01-24 14:19:13,244] [INFO] Query marker FASTA was written to GCF_023703085.1_ASM2370308v1_genomic.fna/markers.fasta
[2024-01-24 14:19:13,245] [INFO] Task started: Blastn
[2024-01-24 14:19:13,245] [INFO] Running command: blastn -query GCF_023703085.1_ASM2370308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1afa81e7-fcd1-4851-bd54-782ca3812039/dqc_reference/reference_markers.fasta -out GCF_023703085.1_ASM2370308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:13,848] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:13,853] [INFO] Selected 29 target genomes.
[2024-01-24 14:19:13,853] [INFO] Target genome list was writen to GCF_023703085.1_ASM2370308v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:13,866] [INFO] Task started: fastANI
[2024-01-24 14:19:13,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg97307b1e-4c96-4e05-ae4d-df25a47a5078/GCF_023703085.1_ASM2370308v1_genomic.fna.gz --refList GCF_023703085.1_ASM2370308v1_genomic.fna/target_genomes.txt --output GCF_023703085.1_ASM2370308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:33,725] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:33,726] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1afa81e7-fcd1-4851-bd54-782ca3812039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:33,726] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1afa81e7-fcd1-4851-bd54-782ca3812039/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:33,737] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:19:33,737] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:19:33,738] [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
Bacillus mycoides	strain=DSM 2048	GCA_022630575.1	1405	1405	type	True	79.2163	53	1451	95	below_threshold
Alkalihalobacterium alkalinitrilicum	strain=DSM 22532	GCA_002019605.1	427920	427920	type	True	78.8042	79	1451	95	below_threshold
Alkalihalobacillus nanhaiisediminis	strain=CGMCC 1.10116	GCA_007830185.1	688079	688079	type	True	77.4814	89	1451	95	below_threshold
Bacillus suaedae	strain=YZJH907-2	GCA_017939705.1	2822140	2822140	type	True	77.2964	97	1451	95	below_threshold
Alkalihalobacillus xiaoxiensis	strain=DSM 21943	GCA_016907895.1	766895	766895	type	True	77.1955	86	1451	95	below_threshold
Desertibacillus haloalkaliphilus	strain=KJ1-10-99	GCA_019039105.1	1328930	1328930	type	True	77.1743	58	1451	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.9511	100	1451	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.9501	101	1451	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	76.949	96	1451	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.898	102	1451	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	76.8894	96	1451	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:33,745] [INFO] DFAST Taxonomy check result was written to GCF_023703085.1_ASM2370308v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:33,746] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:33,746] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:33,747] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1afa81e7-fcd1-4851-bd54-782ca3812039/dqc_reference/checkm_data
[2024-01-24 14:19:33,748] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:33,803] [INFO] Task started: CheckM
[2024-01-24 14:19:33,803] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023703085.1_ASM2370308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023703085.1_ASM2370308v1_genomic.fna/checkm_input GCF_023703085.1_ASM2370308v1_genomic.fna/checkm_result
[2024-01-24 14:20:08,928] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:08,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:08,948] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:08,949] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:08,949] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023703085.1_ASM2370308v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:08,949] [INFO] Task started: Blastn
[2024-01-24 14:20:08,950] [INFO] Running command: blastn -query GCF_023703085.1_ASM2370308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1afa81e7-fcd1-4851-bd54-782ca3812039/dqc_reference/reference_markers_gtdb.fasta -out GCF_023703085.1_ASM2370308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:09,701] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:09,704] [INFO] Selected 30 target genomes.
[2024-01-24 14:20:09,705] [INFO] Target genome list was writen to GCF_023703085.1_ASM2370308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:09,732] [INFO] Task started: fastANI
[2024-01-24 14:20:09,733] [INFO] Running command: fastANI --query /var/lib/cwl/stg97307b1e-4c96-4e05-ae4d-df25a47a5078/GCF_023703085.1_ASM2370308v1_genomic.fna.gz --refList GCF_023703085.1_ASM2370308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023703085.1_ASM2370308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:32,179] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:32,193] [INFO] Found 15 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:20:32,193] [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_016798245.1	s__Alkalihalobacillus_A gibsonii_A	79.8444	589	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900199725.1	s__Cytobacillus massiliigabonensis	79.6316	50	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Cytobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007293315.1	s__Alkalihalobacillus_A sp007293315	79.218	505	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Alkalihalobacillus_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002019605.1	s__Bacillus_BH alkalinitrilicus	78.8042	79	1451	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_000005825.2	s__Bacillus_S pseudofirmus	78.5349	104	1451	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_007830185.1	s__Bacillus_L nanhaiisediminis	77.4814	89	1451	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	77.2505	98	1451	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_016907895.1	s__Bacillus_H xiaoxiensis	77.2271	86	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	97.73	97.69	0.93	0.93	4	-
GCF_019039105.1	s__Desertibacillus haloalkaliphilus	77.1284	59	1451	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	-
GCA_001038565.1	s__Alkalihalobacillus pseudalcaliphilus	77.0446	93	1451	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_000474275.2	s__Bacillus_S marmarensis	76.9511	100	1451	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_000513135.1	s__Bacillus_L akibai	76.9485	102	1451	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_000513095.1	s__Bacillus_L wakoensis	76.9138	95	1451	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_000787375.1	s__Bacillus_L okhensis	76.8374	106	1451	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_001884185.1	s__Bacillus_A albus	76.4773	50	1451	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales;f__Bacillaceae_G;g__Bacillus_A	95.0	97.54	95.46	0.90	0.83	25	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:32,199] [INFO] GTDB search result was written to GCF_023703085.1_ASM2370308v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:32,200] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:32,206] [INFO] DFAST_QC result json was written to GCF_023703085.1_ASM2370308v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:32,206] [INFO] DFAST_QC completed!
[2024-01-24 14:20:32,206] [INFO] Total running time: 0h1m30s