[2024-01-25 20:17:50,413] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:50,415] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:50,415] [INFO] DQC Reference Directory: /var/lib/cwl/stg423e3b62-813d-43bc-8fba-9aac96b306ad/dqc_reference
[2024-01-25 20:17:51,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:51,564] [INFO] Task started: Prodigal
[2024-01-25 20:17:51,564] [INFO] Running command: gunzip -c /var/lib/cwl/stg6512de3b-41e5-46ed-864a-710b19cbca9d/GCF_025234795.1_ASM2523479v1_genomic.fna.gz | prodigal -d GCF_025234795.1_ASM2523479v1_genomic.fna/cds.fna -a GCF_025234795.1_ASM2523479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:58,508] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:58,508] [INFO] Task started: HMMsearch
[2024-01-25 20:17:58,508] [INFO] Running command: hmmsearch --tblout GCF_025234795.1_ASM2523479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg423e3b62-813d-43bc-8fba-9aac96b306ad/dqc_reference/reference_markers.hmm GCF_025234795.1_ASM2523479v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:58,733] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:58,735] [INFO] Found 6/6 markers.
[2024-01-25 20:17:58,762] [INFO] Query marker FASTA was written to GCF_025234795.1_ASM2523479v1_genomic.fna/markers.fasta
[2024-01-25 20:17:58,762] [INFO] Task started: Blastn
[2024-01-25 20:17:58,762] [INFO] Running command: blastn -query GCF_025234795.1_ASM2523479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg423e3b62-813d-43bc-8fba-9aac96b306ad/dqc_reference/reference_markers.fasta -out GCF_025234795.1_ASM2523479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:59,298] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:59,302] [INFO] Selected 11 target genomes.
[2024-01-25 20:17:59,302] [INFO] Target genome list was writen to GCF_025234795.1_ASM2523479v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:59,310] [INFO] Task started: fastANI
[2024-01-25 20:17:59,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg6512de3b-41e5-46ed-864a-710b19cbca9d/GCF_025234795.1_ASM2523479v1_genomic.fna.gz --refList GCF_025234795.1_ASM2523479v1_genomic.fna/target_genomes.txt --output GCF_025234795.1_ASM2523479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:18:05,868] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:05,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg423e3b62-813d-43bc-8fba-9aac96b306ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:18:05,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg423e3b62-813d-43bc-8fba-9aac96b306ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:18:05,876] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:18:05,876] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:18:05,877] [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	93.8696	844	907	95	below_threshold
Exiguobacterium alkaliphilum	strain=12/1	GCA_000714435.1	1428684	1428684	type	True	84.5422	728	907	95	below_threshold
Exiguobacterium aurantiacum	strain=DSM 6208	GCA_000702585.1	33987	33987	type	True	84.5189	726	907	95	below_threshold
Exiguobacterium aurantiacum	strain=NCTC13163	GCA_900450545.1	33987	33987	type	True	84.4978	730	907	95	below_threshold
Exiguobacterium himgiriensis	strain=K22_26	GCA_025234715.1	384621	384621	type	True	83.5156	668	907	95	below_threshold
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	81.1048	498	907	95	below_threshold
Exiguobacterium profundum	strain=10C	GCA_025234635.1	307643	307643	type	True	80.9965	500	907	95	below_threshold
Exiguobacterium marinum	strain=DSM 16307	GCA_000620845.1	273528	273528	type	True	80.936	529	907	95	below_threshold
Exiguobacterium algae	strain=S126	GCA_018617875.1	2751250	2751250	type	True	80.8449	490	907	95	below_threshold
Exiguobacterium qingdaonense	strain=S82	GCA_018617855.1	2751251	2751251	type	True	80.7799	501	907	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:18:05,878] [INFO] DFAST Taxonomy check result was written to GCF_025234795.1_ASM2523479v1_genomic.fna/tc_result.tsv
[2024-01-25 20:18:05,879] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:18:05,879] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:18:05,879] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg423e3b62-813d-43bc-8fba-9aac96b306ad/dqc_reference/checkm_data
[2024-01-25 20:18:05,880] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:18:05,912] [INFO] Task started: CheckM
[2024-01-25 20:18:05,912] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025234795.1_ASM2523479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025234795.1_ASM2523479v1_genomic.fna/checkm_input GCF_025234795.1_ASM2523479v1_genomic.fna/checkm_result
[2024-01-25 20:18:31,091] [INFO] Task succeeded: CheckM
[2024-01-25 20:18:31,092] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:18:31,111] [INFO] ===== Completeness check finished =====
[2024-01-25 20:18:31,111] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:18:31,111] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025234795.1_ASM2523479v1_genomic.fna/markers.fasta)
[2024-01-25 20:18:31,112] [INFO] Task started: Blastn
[2024-01-25 20:18:31,112] [INFO] Running command: blastn -query GCF_025234795.1_ASM2523479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg423e3b62-813d-43bc-8fba-9aac96b306ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_025234795.1_ASM2523479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:18:31,912] [INFO] Task succeeded: Blastn
[2024-01-25 20:18:31,914] [INFO] Selected 8 target genomes.
[2024-01-25 20:18:31,915] [INFO] Target genome list was writen to GCF_025234795.1_ASM2523479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:18:31,922] [INFO] Task started: fastANI
[2024-01-25 20:18:31,922] [INFO] Running command: fastANI --query /var/lib/cwl/stg6512de3b-41e5-46ed-864a-710b19cbca9d/GCF_025234795.1_ASM2523479v1_genomic.fna.gz --refList GCF_025234795.1_ASM2523479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025234795.1_ASM2523479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:18:37,490] [INFO] Task succeeded: fastANI
[2024-01-25 20:18:37,496] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:18:37,497] [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	99.9999	906	907	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	93.8696	844	907	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	92.7968	817	907	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	91.2606	774	907	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	90.3785	741	907	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	89.8107	755	907	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	89.4074	810	907	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	84.5189	726	907	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 20:18:37,498] [INFO] GTDB search result was written to GCF_025234795.1_ASM2523479v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:18:37,498] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:18:37,501] [INFO] DFAST_QC result json was written to GCF_025234795.1_ASM2523479v1_genomic.fna/dqc_result.json
[2024-01-25 20:18:37,501] [INFO] DFAST_QC completed!
[2024-01-25 20:18:37,501] [INFO] Total running time: 0h0m47s