[2024-01-24 13:22:10,901] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:10,903] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:10,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg725f068c-ac66-40d8-b6a2-3a8207c92536/dqc_reference
[2024-01-24 13:22:12,222] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:12,224] [INFO] Task started: Prodigal
[2024-01-24 13:22:12,224] [INFO] Running command: gunzip -c /var/lib/cwl/stg82f541da-bfa9-4bb4-abcb-4e9379f07b50/GCF_016907895.1_ASM1690789v1_genomic.fna.gz | prodigal -d GCF_016907895.1_ASM1690789v1_genomic.fna/cds.fna -a GCF_016907895.1_ASM1690789v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:22,456] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:22,456] [INFO] Task started: HMMsearch
[2024-01-24 13:22:22,457] [INFO] Running command: hmmsearch --tblout GCF_016907895.1_ASM1690789v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg725f068c-ac66-40d8-b6a2-3a8207c92536/dqc_reference/reference_markers.hmm GCF_016907895.1_ASM1690789v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:22,829] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:22,830] [INFO] Found 6/6 markers.
[2024-01-24 13:22:22,886] [INFO] Query marker FASTA was written to GCF_016907895.1_ASM1690789v1_genomic.fna/markers.fasta
[2024-01-24 13:22:22,887] [INFO] Task started: Blastn
[2024-01-24 13:22:22,887] [INFO] Running command: blastn -query GCF_016907895.1_ASM1690789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg725f068c-ac66-40d8-b6a2-3a8207c92536/dqc_reference/reference_markers.fasta -out GCF_016907895.1_ASM1690789v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:23,460] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:23,463] [INFO] Selected 20 target genomes.
[2024-01-24 13:22:23,464] [INFO] Target genome list was writen to GCF_016907895.1_ASM1690789v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:23,469] [INFO] Task started: fastANI
[2024-01-24 13:22:23,469] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f541da-bfa9-4bb4-abcb-4e9379f07b50/GCF_016907895.1_ASM1690789v1_genomic.fna.gz --refList GCF_016907895.1_ASM1690789v1_genomic.fna/target_genomes.txt --output GCF_016907895.1_ASM1690789v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:36,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:36,155] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg725f068c-ac66-40d8-b6a2-3a8207c92536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:36,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg725f068c-ac66-40d8-b6a2-3a8207c92536/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:36,164] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:22:36,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:22:36,165] [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 xiaoxiensis	strain=DSM 21943	GCA_016907895.1	766895	766895	type	True	100.0	1437	1437	95	conclusive
Alkalihalobacillus patagoniensis	strain=DSM 16117	GCA_002019705.1	228576	228576	type	True	78.9911	324	1437	95	below_threshold
Alkalihalobacillus clausii	strain=DSM 8716	GCA_002250115.1	79880	79880	suspected-type	True	77.7607	154	1437	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_000513095.1	127891	127891	type	True	77.144	77	1437	95	below_threshold
Alkalihalobacillus wakoensis	strain=JCM 9140	GCA_001315045.1	127891	127891	type	True	77.0825	77	1437	95	below_threshold
Alkalihalophilus marmarensis	strain=DSM 21297	GCA_000474275.2	521377	521377	type	True	76.9264	66	1437	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_001315085.1	1411	1411	type	True	76.8931	72	1437	95	below_threshold
Alkalihalobacillus akibai	strain=JCM 9157	GCA_000513135.1	1411	1411	type	True	76.8913	71	1437	95	below_threshold
Anaerobacillus alkalidiazotrophicus	strain=DSM 22531	GCA_001866055.1	472963	472963	type	True	76.7132	56	1437	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:36,166] [INFO] DFAST Taxonomy check result was written to GCF_016907895.1_ASM1690789v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:36,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:36,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:36,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg725f068c-ac66-40d8-b6a2-3a8207c92536/dqc_reference/checkm_data
[2024-01-24 13:22:36,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:36,215] [INFO] Task started: CheckM
[2024-01-24 13:22:36,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016907895.1_ASM1690789v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016907895.1_ASM1690789v1_genomic.fna/checkm_input GCF_016907895.1_ASM1690789v1_genomic.fna/checkm_result
[2024-01-24 13:23:09,831] [INFO] Task succeeded: CheckM
[2024-01-24 13:23:09,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:23:09,851] [INFO] ===== Completeness check finished =====
[2024-01-24 13:23:09,852] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:23:09,852] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016907895.1_ASM1690789v1_genomic.fna/markers.fasta)
[2024-01-24 13:23:09,852] [INFO] Task started: Blastn
[2024-01-24 13:23:09,853] [INFO] Running command: blastn -query GCF_016907895.1_ASM1690789v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg725f068c-ac66-40d8-b6a2-3a8207c92536/dqc_reference/reference_markers_gtdb.fasta -out GCF_016907895.1_ASM1690789v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:23:10,648] [INFO] Task succeeded: Blastn
[2024-01-24 13:23:10,651] [INFO] Selected 19 target genomes.
[2024-01-24 13:23:10,652] [INFO] Target genome list was writen to GCF_016907895.1_ASM1690789v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:23:10,723] [INFO] Task started: fastANI
[2024-01-24 13:23:10,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg82f541da-bfa9-4bb4-abcb-4e9379f07b50/GCF_016907895.1_ASM1690789v1_genomic.fna.gz --refList GCF_016907895.1_ASM1690789v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016907895.1_ASM1690789v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:24,609] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:24,623] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:24,623] [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_016907895.1	s__Bacillus_H xiaoxiensis	100.0	1437	1437	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	conclusive
GCF_002019705.1	s__Bacillus_H patagoniensis	78.9953	325	1437	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_007725405.1	s__Bacillus_H miscanthi	78.9891	281	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	99.10	99.10	0.94	0.93	3	-
GCF_900197585.1	s__Bacillus_H sp900197585	78.69	267	1437	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_002019765.1	s__Bacillus_H oshimensis	78.6735	287	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.0	98.95	98.65	0.95	0.93	6	-
GCA_001310375.1	s__Bacillus_H sp001310375	78.465	312	1437	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_002250115.1	s__Bacillus_H clausii	77.7526	153	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.4953	98.66	98.17	0.95	0.92	12	-
GCF_900142675.1	s__Bacillus_H rhizosphaerae	77.5607	171	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Bacillaceae_D;g__Bacillus_H	95.4953	99.26	98.97	0.95	0.94	22	-
GCF_000513095.1	s__Bacillus_L wakoensis	77.1279	76	1437	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_000513135.1	s__Bacillus_L akibai	76.8931	72	1437	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_002335805.1	s__FJAT-45350 sp002335805	76.7156	60	1437	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_001866055.1	s__Anaerobacillus alkalidiazotrophicus	76.6786	56	1437	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_H;f__Anaerobacillaceae;g__Anaerobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:24,628] [INFO] GTDB search result was written to GCF_016907895.1_ASM1690789v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:24,628] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:24,631] [INFO] DFAST_QC result json was written to GCF_016907895.1_ASM1690789v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:24,632] [INFO] DFAST_QC completed!
[2024-01-24 13:23:24,632] [INFO] Total running time: 0h1m14s