[2024-01-24 13:48:43,338] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:43,340] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:43,340] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bb7b4c6-a530-4c62-993c-64e559d832a6/dqc_reference
[2024-01-24 13:48:44,588] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:48:44,589] [INFO] Task started: Prodigal
[2024-01-24 13:48:44,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg8a15b872-1585-4eb9-842d-1b5834f9493c/GCF_000620845.1_ASM62084v1_genomic.fna.gz | prodigal -d GCF_000620845.1_ASM62084v1_genomic.fna/cds.fna -a GCF_000620845.1_ASM62084v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:48:52,427] [INFO] Task succeeded: Prodigal
[2024-01-24 13:48:52,427] [INFO] Task started: HMMsearch
[2024-01-24 13:48:52,428] [INFO] Running command: hmmsearch --tblout GCF_000620845.1_ASM62084v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bb7b4c6-a530-4c62-993c-64e559d832a6/dqc_reference/reference_markers.hmm GCF_000620845.1_ASM62084v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:48:52,674] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:48:52,675] [INFO] Found 6/6 markers.
[2024-01-24 13:48:52,704] [INFO] Query marker FASTA was written to GCF_000620845.1_ASM62084v1_genomic.fna/markers.fasta
[2024-01-24 13:48:52,705] [INFO] Task started: Blastn
[2024-01-24 13:48:52,705] [INFO] Running command: blastn -query GCF_000620845.1_ASM62084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bb7b4c6-a530-4c62-993c-64e559d832a6/dqc_reference/reference_markers.fasta -out GCF_000620845.1_ASM62084v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:48:53,277] [INFO] Task succeeded: Blastn
[2024-01-24 13:48:53,281] [INFO] Selected 7 target genomes.
[2024-01-24 13:48:53,282] [INFO] Target genome list was writen to GCF_000620845.1_ASM62084v1_genomic.fna/target_genomes.txt
[2024-01-24 13:48:53,286] [INFO] Task started: fastANI
[2024-01-24 13:48:53,286] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a15b872-1585-4eb9-842d-1b5834f9493c/GCF_000620845.1_ASM62084v1_genomic.fna.gz --refList GCF_000620845.1_ASM62084v1_genomic.fna/target_genomes.txt --output GCF_000620845.1_ASM62084v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:48:58,001] [INFO] Task succeeded: fastANI
[2024-01-24 13:48:58,001] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bb7b4c6-a530-4c62-993c-64e559d832a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:48:58,002] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bb7b4c6-a530-4c62-993c-64e559d832a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:48:58,013] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:48:58,013] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:48:58,013] [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 marinum	strain=DSM 16307	GCA_000620845.1	273528	273528	type	True	99.9895	934	937	95	conclusive
Exiguobacterium profundum	strain=10C	GCA_025234635.1	307643	307643	type	True	88.233	751	937	95	below_threshold
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	87.5675	736	937	95	below_threshold
Exiguobacterium qingdaonense	strain=S82	GCA_018617855.1	2751251	2751251	type	True	87.1972	795	937	95	below_threshold
Exiguobacterium algae	strain=S126	GCA_018617875.1	2751250	2751250	type	True	82.8506	584	937	95	below_threshold
Exiguobacterium chiriqhucha	strain=RW-2	GCA_000416965.1	1385984	1385984	type	True	81.0054	551	937	95	below_threshold
Exiguobacterium himgiriensis	strain=K22_26	GCA_025234715.1	384621	384621	type	True	80.7516	488	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:48:58,015] [INFO] DFAST Taxonomy check result was written to GCF_000620845.1_ASM62084v1_genomic.fna/tc_result.tsv
[2024-01-24 13:48:58,016] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:48:58,016] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:48:58,016] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bb7b4c6-a530-4c62-993c-64e559d832a6/dqc_reference/checkm_data
[2024-01-24 13:48:58,017] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:48:58,045] [INFO] Task started: CheckM
[2024-01-24 13:48:58,045] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000620845.1_ASM62084v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000620845.1_ASM62084v1_genomic.fna/checkm_input GCF_000620845.1_ASM62084v1_genomic.fna/checkm_result
[2024-01-24 13:49:27,230] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:27,232] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:27,253] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:27,253] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:27,254] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000620845.1_ASM62084v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:27,254] [INFO] Task started: Blastn
[2024-01-24 13:49:27,254] [INFO] Running command: blastn -query GCF_000620845.1_ASM62084v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bb7b4c6-a530-4c62-993c-64e559d832a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_000620845.1_ASM62084v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:27,998] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:28,003] [INFO] Selected 7 target genomes.
[2024-01-24 13:49:28,004] [INFO] Target genome list was writen to GCF_000620845.1_ASM62084v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:28,010] [INFO] Task started: fastANI
[2024-01-24 13:49:28,010] [INFO] Running command: fastANI --query /var/lib/cwl/stg8a15b872-1585-4eb9-842d-1b5834f9493c/GCF_000620845.1_ASM62084v1_genomic.fna.gz --refList GCF_000620845.1_ASM62084v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000620845.1_ASM62084v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:32,947] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:32,959] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:32,959] [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_000620845.1	s__Exiguobacterium marinum	99.9895	934	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.37	97.95	0.94	0.94	10	conclusive
GCF_001909285.1	s__Exiguobacterium profundum_A	88.2677	805	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.55	95.32	0.92	0.88	29	-
GCF_018617395.1	s__Exiguobacterium sp018617395	87.8453	789	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	97.92	96.72	0.94	0.91	3	-
GCA_902362975.1	s__Exiguobacterium sp902362975	87.8321	736	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.52	95.12	0.85	0.82	3	-
GCF_018617485.1	s__Exiguobacterium sp018617485	87.5938	804	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.75	95.34	0.91	0.90	6	-
GCF_001908175.1	s__Exiguobacterium sp001908175	87.5272	758	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.57	95.32	0.91	0.90	6	-
GCF_018617855.1	s__Exiguobacterium sp018617855	87.1972	795	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:32,961] [INFO] GTDB search result was written to GCF_000620845.1_ASM62084v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:32,962] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:32,965] [INFO] DFAST_QC result json was written to GCF_000620845.1_ASM62084v1_genomic.fna/dqc_result.json
[2024-01-24 13:49:32,965] [INFO] DFAST_QC completed!
[2024-01-24 13:49:32,965] [INFO] Total running time: 0h0m50s