[2024-01-24 14:22:02,852] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:02,855] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:02,855] [INFO] DQC Reference Directory: /var/lib/cwl/stg31e80214-f0fe-4c9e-a06c-86815a1f9e9a/dqc_reference
[2024-01-24 14:22:04,331] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:04,332] [INFO] Task started: Prodigal
[2024-01-24 14:22:04,332] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0861271-ee63-42c9-acd8-0f39a4082e0c/GCF_018617875.1_ASM1861787v1_genomic.fna.gz | prodigal -d GCF_018617875.1_ASM1861787v1_genomic.fna/cds.fna -a GCF_018617875.1_ASM1861787v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:22:12,424] [INFO] Task succeeded: Prodigal
[2024-01-24 14:22:12,425] [INFO] Task started: HMMsearch
[2024-01-24 14:22:12,425] [INFO] Running command: hmmsearch --tblout GCF_018617875.1_ASM1861787v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg31e80214-f0fe-4c9e-a06c-86815a1f9e9a/dqc_reference/reference_markers.hmm GCF_018617875.1_ASM1861787v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:22:12,720] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:22:12,722] [INFO] Found 6/6 markers.
[2024-01-24 14:22:12,771] [INFO] Query marker FASTA was written to GCF_018617875.1_ASM1861787v1_genomic.fna/markers.fasta
[2024-01-24 14:22:12,772] [INFO] Task started: Blastn
[2024-01-24 14:22:12,772] [INFO] Running command: blastn -query GCF_018617875.1_ASM1861787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e80214-f0fe-4c9e-a06c-86815a1f9e9a/dqc_reference/reference_markers.fasta -out GCF_018617875.1_ASM1861787v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:13,485] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:13,488] [INFO] Selected 9 target genomes.
[2024-01-24 14:22:13,489] [INFO] Target genome list was writen to GCF_018617875.1_ASM1861787v1_genomic.fna/target_genomes.txt
[2024-01-24 14:22:13,499] [INFO] Task started: fastANI
[2024-01-24 14:22:13,499] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0861271-ee63-42c9-acd8-0f39a4082e0c/GCF_018617875.1_ASM1861787v1_genomic.fna.gz --refList GCF_018617875.1_ASM1861787v1_genomic.fna/target_genomes.txt --output GCF_018617875.1_ASM1861787v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:22:19,589] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:19,589] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg31e80214-f0fe-4c9e-a06c-86815a1f9e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:22:19,589] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg31e80214-f0fe-4c9e-a06c-86815a1f9e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:22:19,599] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:22:19,599] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:22:19,599] [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 algae	strain=S126	GCA_018617875.1	2751250	2751250	type	True	100.0	860	862	95	conclusive
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	83.096	553	862	95	below_threshold
Exiguobacterium marinum	strain=DSM 16307	GCA_000620845.1	273528	273528	type	True	82.9036	590	862	95	below_threshold
Exiguobacterium profundum	strain=10C	GCA_025234635.1	307643	307643	type	True	82.8018	555	862	95	below_threshold
Exiguobacterium qingdaonense	strain=S82	GCA_018617855.1	2751251	2751251	type	True	82.4768	577	862	95	below_threshold
Exiguobacterium chiriqhucha	strain=RW-2	GCA_000416965.1	1385984	1385984	type	True	80.9649	512	862	95	below_threshold
Exiguobacterium aurantiacum	strain=DSM 6208	GCA_000702585.1	33987	33987	type	True	80.9605	501	862	95	below_threshold
Exiguobacterium aurantiacum	strain=NCTC13163	GCA_900450545.1	33987	33987	type	True	80.8588	511	862	95	below_threshold
Exiguobacterium himgiriensis	strain=K22_26	GCA_025234715.1	384621	384621	type	True	80.8462	441	862	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:22:19,601] [INFO] DFAST Taxonomy check result was written to GCF_018617875.1_ASM1861787v1_genomic.fna/tc_result.tsv
[2024-01-24 14:22:19,601] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:22:19,602] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:22:19,602] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg31e80214-f0fe-4c9e-a06c-86815a1f9e9a/dqc_reference/checkm_data
[2024-01-24 14:22:19,603] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:22:19,631] [INFO] Task started: CheckM
[2024-01-24 14:22:19,632] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018617875.1_ASM1861787v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018617875.1_ASM1861787v1_genomic.fna/checkm_input GCF_018617875.1_ASM1861787v1_genomic.fna/checkm_result
[2024-01-24 14:22:49,117] [INFO] Task succeeded: CheckM
[2024-01-24 14:22:49,118] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:22:49,139] [INFO] ===== Completeness check finished =====
[2024-01-24 14:22:49,139] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:22:49,140] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018617875.1_ASM1861787v1_genomic.fna/markers.fasta)
[2024-01-24 14:22:49,140] [INFO] Task started: Blastn
[2024-01-24 14:22:49,140] [INFO] Running command: blastn -query GCF_018617875.1_ASM1861787v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg31e80214-f0fe-4c9e-a06c-86815a1f9e9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_018617875.1_ASM1861787v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:22:49,938] [INFO] Task succeeded: Blastn
[2024-01-24 14:22:49,942] [INFO] Selected 11 target genomes.
[2024-01-24 14:22:49,942] [INFO] Target genome list was writen to GCF_018617875.1_ASM1861787v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:22:49,955] [INFO] Task started: fastANI
[2024-01-24 14:22:49,955] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0861271-ee63-42c9-acd8-0f39a4082e0c/GCF_018617875.1_ASM1861787v1_genomic.fna.gz --refList GCF_018617875.1_ASM1861787v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018617875.1_ASM1861787v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:22:56,916] [INFO] Task succeeded: fastANI
[2024-01-24 14:22:56,933] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:22:56,933] [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_018617875.1	s__Exiguobacterium sp018617875	100.0	860	862	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_018617485.1	s__Exiguobacterium sp018617485	83.3134	585	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.75	95.34	0.91	0.90	6	-
GCF_018617395.1	s__Exiguobacterium sp018617395	83.1866	585	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	97.92	96.72	0.94	0.91	3	-
GCF_001908175.1	s__Exiguobacterium sp001908175	83.0146	589	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.57	95.32	0.91	0.90	6	-
GCF_001909285.1	s__Exiguobacterium profundum_A	83.0015	598	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.55	95.32	0.92	0.88	29	-
GCF_000620845.1	s__Exiguobacterium marinum	82.918	589	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.37	97.95	0.94	0.94	10	-
GCA_902362975.1	s__Exiguobacterium sp902362975	82.8034	538	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.52	95.12	0.85	0.82	3	-
GCF_018617855.1	s__Exiguobacterium sp018617855	82.4862	576	862	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	81.0146	507	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.45	98.45	0.95	0.95	2	-
GCF_018618475.1	s__Exiguobacterium sp018618475	80.952	470	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001766415.1	s__Exiguobacterium aurantiacum_A	80.5939	511	862	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	97.50	95.33	0.91	0.84	17	-
--------------------------------------------------------------------------------
[2024-01-24 14:22:56,936] [INFO] GTDB search result was written to GCF_018617875.1_ASM1861787v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:22:56,937] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:22:56,941] [INFO] DFAST_QC result json was written to GCF_018617875.1_ASM1861787v1_genomic.fna/dqc_result.json
[2024-01-24 14:22:56,941] [INFO] DFAST_QC completed!
[2024-01-24 14:22:56,941] [INFO] Total running time: 0h0m54s