[2024-01-24 12:00:36,713] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:00:36,716] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:00:36,716] [INFO] DQC Reference Directory: /var/lib/cwl/stg2f605252-bf5d-4691-8fff-484735411f8f/dqc_reference
[2024-01-24 12:00:39,376] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:00:39,377] [INFO] Task started: Prodigal
[2024-01-24 12:00:39,378] [INFO] Running command: gunzip -c /var/lib/cwl/stg089a89d1-95d8-4e9f-bc95-283121bdffc0/GCF_006861825.1_ASM686182v1_genomic.fna.gz | prodigal -d GCF_006861825.1_ASM686182v1_genomic.fna/cds.fna -a GCF_006861825.1_ASM686182v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:47,047] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:47,048] [INFO] Task started: HMMsearch
[2024-01-24 12:00:47,048] [INFO] Running command: hmmsearch --tblout GCF_006861825.1_ASM686182v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2f605252-bf5d-4691-8fff-484735411f8f/dqc_reference/reference_markers.hmm GCF_006861825.1_ASM686182v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:47,311] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:47,312] [INFO] Found 6/6 markers.
[2024-01-24 12:00:47,346] [INFO] Query marker FASTA was written to GCF_006861825.1_ASM686182v1_genomic.fna/markers.fasta
[2024-01-24 12:00:47,347] [INFO] Task started: Blastn
[2024-01-24 12:00:47,347] [INFO] Running command: blastn -query GCF_006861825.1_ASM686182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f605252-bf5d-4691-8fff-484735411f8f/dqc_reference/reference_markers.fasta -out GCF_006861825.1_ASM686182v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:47,935] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:47,940] [INFO] Selected 14 target genomes.
[2024-01-24 12:00:47,940] [INFO] Target genome list was writen to GCF_006861825.1_ASM686182v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:47,949] [INFO] Task started: fastANI
[2024-01-24 12:00:47,949] [INFO] Running command: fastANI --query /var/lib/cwl/stg089a89d1-95d8-4e9f-bc95-283121bdffc0/GCF_006861825.1_ASM686182v1_genomic.fna.gz --refList GCF_006861825.1_ASM686182v1_genomic.fna/target_genomes.txt --output GCF_006861825.1_ASM686182v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:01:00,514] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:00,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2f605252-bf5d-4691-8fff-484735411f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:01:00,515] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2f605252-bf5d-4691-8fff-484735411f8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:01:00,524] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:01:00,524] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:01:00,524] [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
Psychrobacillus vulpis	strain=Z8	GCA_006861825.1	2325572	2325572	type	True	100.0	1299	1300	95	conclusive
Psychrobacillus glaciei	strain=PB01	GCA_008973485.1	2283160	2283160	type	True	80.9191	674	1300	95	below_threshold
Psychrobacillus soli	strain=NHI-2	GCA_006861775.1	1543965	1543965	type	True	80.7709	630	1300	95	below_threshold
Psychrobacillus lasiicapitis	strain=NEAU-3TGS17	GCA_006861795.1	1636719	1636719	type	True	80.6319	633	1300	95	below_threshold
Psychrobacillus lasiicapitis	strain=CGMCC 1.15308	GCA_014641675.1	1636719	1636719	type	True	80.5164	646	1300	95	below_threshold
Psychrobacillus insolitus	strain=DSM 5	GCA_003254155.1	1461	1461	type	True	79.5882	437	1300	95	below_threshold
Psychrobacillus psychrotolerans	strain=DSM 11706	GCA_900115805.1	126156	126156	type	True	79.5553	421	1300	95	below_threshold
Psychrobacillus faecigallinarum	strain=Sa2BUA9	GCA_014836595.1	2762235	2762235	type	True	79.3568	373	1300	95	below_threshold
Caryophanon latum	strain=DSM 14151	GCA_001700325.1	33977	33977	type	True	78.8706	60	1300	95	below_threshold
Niallia alba	strain=UniB3	GCA_012933555.1	2729105	2729105	type	True	77.2479	74	1300	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:01:00,526] [INFO] DFAST Taxonomy check result was written to GCF_006861825.1_ASM686182v1_genomic.fna/tc_result.tsv
[2024-01-24 12:01:00,527] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:01:00,527] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:01:00,527] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2f605252-bf5d-4691-8fff-484735411f8f/dqc_reference/checkm_data
[2024-01-24 12:01:00,528] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:01:00,567] [INFO] Task started: CheckM
[2024-01-24 12:01:00,568] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006861825.1_ASM686182v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006861825.1_ASM686182v1_genomic.fna/checkm_input GCF_006861825.1_ASM686182v1_genomic.fna/checkm_result
[2024-01-24 12:01:29,024] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:29,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:29,053] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:29,054] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:29,054] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006861825.1_ASM686182v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:29,055] [INFO] Task started: Blastn
[2024-01-24 12:01:29,055] [INFO] Running command: blastn -query GCF_006861825.1_ASM686182v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2f605252-bf5d-4691-8fff-484735411f8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_006861825.1_ASM686182v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:29,808] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:29,813] [INFO] Selected 11 target genomes.
[2024-01-24 12:01:29,813] [INFO] Target genome list was writen to GCF_006861825.1_ASM686182v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:29,823] [INFO] Task started: fastANI
[2024-01-24 12:01:29,823] [INFO] Running command: fastANI --query /var/lib/cwl/stg089a89d1-95d8-4e9f-bc95-283121bdffc0/GCF_006861825.1_ASM686182v1_genomic.fna.gz --refList GCF_006861825.1_ASM686182v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006861825.1_ASM686182v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:42,405] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:42,417] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:42,417] [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_006861825.1	s__Psychrobacillus vulpis	100.0	1299	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001278755.1	s__Psychrobacillus sp001278755	81.253	672	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	97.52	97.52	0.91	0.91	2	-
GCF_008973485.1	s__Psychrobacillus glaciei	80.9112	674	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861775.1	s__Psychrobacillus soli	80.7714	630	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900111345.1	s__Psychrobacillus sp900111345	80.6456	657	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006861795.1	s__Psychrobacillus lasiicapitis	80.6225	634	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCF_007676755.1	s__Psychrobacillus sp007676755	80.4988	628	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254155.1	s__Psychrobacillus insolitus	79.588	437	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Psychrobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002237755.1	s__Lysinibacillus sp002237755	77.9959	141	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_A;f__Planococcaceae;g__Lysinibacillus	95.0	96.32	95.08	0.88	0.84	5	-
GCA_019219025.1	s__Neobacillus sp019219025	77.675	87	1300	d__Bacteria;p__Firmicutes;c__Bacilli;o__Bacillales_B;f__DSM-18226;g__Neobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:42,419] [INFO] GTDB search result was written to GCF_006861825.1_ASM686182v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:42,419] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:42,422] [INFO] DFAST_QC result json was written to GCF_006861825.1_ASM686182v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:42,422] [INFO] DFAST_QC completed!
[2024-01-24 12:01:42,423] [INFO] Total running time: 0h1m6s