[2024-01-25 18:02:05,843] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:02:05,845] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:02:05,845] [INFO] DQC Reference Directory: /var/lib/cwl/stg434766b8-5055-4397-984e-fde13329794c/dqc_reference
[2024-01-25 18:02:06,973] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:02:06,973] [INFO] Task started: Prodigal
[2024-01-25 18:02:06,974] [INFO] Running command: gunzip -c /var/lib/cwl/stge2e88b60-5250-4d00-a027-3fea895d84ee/GCF_025234665.1_ASM2523466v1_genomic.fna.gz | prodigal -d GCF_025234665.1_ASM2523466v1_genomic.fna/cds.fna -a GCF_025234665.1_ASM2523466v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:02:14,031] [INFO] Task succeeded: Prodigal
[2024-01-25 18:02:14,031] [INFO] Task started: HMMsearch
[2024-01-25 18:02:14,031] [INFO] Running command: hmmsearch --tblout GCF_025234665.1_ASM2523466v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg434766b8-5055-4397-984e-fde13329794c/dqc_reference/reference_markers.hmm GCF_025234665.1_ASM2523466v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:02:14,254] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:02:14,255] [INFO] Found 6/6 markers.
[2024-01-25 18:02:14,280] [INFO] Query marker FASTA was written to GCF_025234665.1_ASM2523466v1_genomic.fna/markers.fasta
[2024-01-25 18:02:14,280] [INFO] Task started: Blastn
[2024-01-25 18:02:14,280] [INFO] Running command: blastn -query GCF_025234665.1_ASM2523466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg434766b8-5055-4397-984e-fde13329794c/dqc_reference/reference_markers.fasta -out GCF_025234665.1_ASM2523466v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:14,834] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:14,837] [INFO] Selected 11 target genomes.
[2024-01-25 18:02:14,837] [INFO] Target genome list was writen to GCF_025234665.1_ASM2523466v1_genomic.fna/target_genomes.txt
[2024-01-25 18:02:14,845] [INFO] Task started: fastANI
[2024-01-25 18:02:14,845] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e88b60-5250-4d00-a027-3fea895d84ee/GCF_025234665.1_ASM2523466v1_genomic.fna.gz --refList GCF_025234665.1_ASM2523466v1_genomic.fna/target_genomes.txt --output GCF_025234665.1_ASM2523466v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:02:21,632] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:21,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg434766b8-5055-4397-984e-fde13329794c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:02:21,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg434766b8-5055-4397-984e-fde13329794c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:02:21,640] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 18:02:21,641] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 18:02:21,641] [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
Exiguobacterium chiriqhucha	strain=RW-2	GCA_000416965.1	1385984	1385984	type	True	93.9003	850	909	95	below_threshold
Exiguobacterium aurantiacum	strain=DSM 6208	GCA_000702585.1	33987	33987	type	True	84.5711	720	909	95	below_threshold
Exiguobacterium aurantiacum	strain=NCTC13163	GCA_900450545.1	33987	33987	type	True	84.5625	731	909	95	below_threshold
Exiguobacterium alkaliphilum	strain=12/1	GCA_000714435.1	1428684	1428684	type	True	84.5224	721	909	95	below_threshold
Exiguobacterium himgiriensis	strain=K22_26	GCA_025234715.1	384621	384621	type	True	83.4456	670	909	95	below_threshold
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	81.2709	483	909	95	below_threshold
Exiguobacterium marinum	strain=DSM 16307	GCA_000620845.1	273528	273528	type	True	81.0763	519	909	95	below_threshold
Exiguobacterium profundum	strain=10C	GCA_025234635.1	307643	307643	type	True	80.9923	504	909	95	below_threshold
Exiguobacterium algae	strain=S126	GCA_018617875.1	2751250	2751250	type	True	80.7987	499	909	95	below_threshold
Exiguobacterium qingdaonense	strain=S82	GCA_018617855.1	2751251	2751251	type	True	80.7294	508	909	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:02:21,655] [INFO] DFAST Taxonomy check result was written to GCF_025234665.1_ASM2523466v1_genomic.fna/tc_result.tsv
[2024-01-25 18:02:21,656] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:02:21,656] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:02:21,656] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg434766b8-5055-4397-984e-fde13329794c/dqc_reference/checkm_data
[2024-01-25 18:02:21,657] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:02:21,689] [INFO] Task started: CheckM
[2024-01-25 18:02:21,689] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025234665.1_ASM2523466v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025234665.1_ASM2523466v1_genomic.fna/checkm_input GCF_025234665.1_ASM2523466v1_genomic.fna/checkm_result
[2024-01-25 18:02:46,575] [INFO] Task succeeded: CheckM
[2024-01-25 18:02:46,576] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:02:46,591] [INFO] ===== Completeness check finished =====
[2024-01-25 18:02:46,591] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:02:46,591] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025234665.1_ASM2523466v1_genomic.fna/markers.fasta)
[2024-01-25 18:02:46,592] [INFO] Task started: Blastn
[2024-01-25 18:02:46,592] [INFO] Running command: blastn -query GCF_025234665.1_ASM2523466v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg434766b8-5055-4397-984e-fde13329794c/dqc_reference/reference_markers_gtdb.fasta -out GCF_025234665.1_ASM2523466v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:02:47,368] [INFO] Task succeeded: Blastn
[2024-01-25 18:02:47,372] [INFO] Selected 8 target genomes.
[2024-01-25 18:02:47,372] [INFO] Target genome list was writen to GCF_025234665.1_ASM2523466v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:02:47,378] [INFO] Task started: fastANI
[2024-01-25 18:02:47,378] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e88b60-5250-4d00-a027-3fea895d84ee/GCF_025234665.1_ASM2523466v1_genomic.fna.gz --refList GCF_025234665.1_ASM2523466v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025234665.1_ASM2523466v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:02:53,194] [INFO] Task succeeded: fastANI
[2024-01-25 18:02:53,201] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:02:53,201] [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_018616375.1	s__Exiguobacterium sp018616375	99.9998	906	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000416965.1	s__Exiguobacterium chiriqhucha	93.9003	850	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.87	95.58	0.92	0.89	18	-
GCF_018618415.1	s__Exiguobacterium sp018618415	92.8288	815	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003467445.1	s__Exiguobacterium sp003467445	91.3035	770	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005960665.1	s__Exiguobacterium mexicanum	90.4452	748	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	97.16	96.68	0.89	0.87	17	-
GCF_003331145.1	s__Exiguobacterium sp003331145	89.8319	759	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004336985.1	s__Exiguobacterium sp004336985	89.5032	809	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.45	98.45	0.95	0.95	2	-
GCF_000702585.1	s__Exiguobacterium aurantiacum	84.5711	720	909	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.63	97.93	0.96	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 18:02:53,202] [INFO] GTDB search result was written to GCF_025234665.1_ASM2523466v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:02:53,203] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:02:53,206] [INFO] DFAST_QC result json was written to GCF_025234665.1_ASM2523466v1_genomic.fna/dqc_result.json
[2024-01-25 18:02:53,207] [INFO] DFAST_QC completed!
[2024-01-25 18:02:53,207] [INFO] Total running time: 0h0m47s