[2024-01-24 12:34:20,425] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:34:20,428] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:34:20,428] [INFO] DQC Reference Directory: /var/lib/cwl/stgb6387e4c-cd7b-4e66-a8f2-670e79c34161/dqc_reference
[2024-01-24 12:34:21,641] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:34:21,642] [INFO] Task started: Prodigal
[2024-01-24 12:34:21,642] [INFO] Running command: gunzip -c /var/lib/cwl/stgccc7a0c0-2527-4bb6-9e56-8be58207156b/GCF_018617855.1_ASM1861785v1_genomic.fna.gz | prodigal -d GCF_018617855.1_ASM1861785v1_genomic.fna/cds.fna -a GCF_018617855.1_ASM1861785v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:34:29,131] [INFO] Task succeeded: Prodigal
[2024-01-24 12:34:29,132] [INFO] Task started: HMMsearch
[2024-01-24 12:34:29,132] [INFO] Running command: hmmsearch --tblout GCF_018617855.1_ASM1861785v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb6387e4c-cd7b-4e66-a8f2-670e79c34161/dqc_reference/reference_markers.hmm GCF_018617855.1_ASM1861785v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:34:29,400] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:34:29,401] [INFO] Found 6/6 markers.
[2024-01-24 12:34:29,427] [INFO] Query marker FASTA was written to GCF_018617855.1_ASM1861785v1_genomic.fna/markers.fasta
[2024-01-24 12:34:29,428] [INFO] Task started: Blastn
[2024-01-24 12:34:29,428] [INFO] Running command: blastn -query GCF_018617855.1_ASM1861785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6387e4c-cd7b-4e66-a8f2-670e79c34161/dqc_reference/reference_markers.fasta -out GCF_018617855.1_ASM1861785v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:34:29,992] [INFO] Task succeeded: Blastn
[2024-01-24 12:34:29,995] [INFO] Selected 8 target genomes.
[2024-01-24 12:34:29,996] [INFO] Target genome list was writen to GCF_018617855.1_ASM1861785v1_genomic.fna/target_genomes.txt
[2024-01-24 12:34:29,999] [INFO] Task started: fastANI
[2024-01-24 12:34:29,999] [INFO] Running command: fastANI --query /var/lib/cwl/stgccc7a0c0-2527-4bb6-9e56-8be58207156b/GCF_018617855.1_ASM1861785v1_genomic.fna.gz --refList GCF_018617855.1_ASM1861785v1_genomic.fna/target_genomes.txt --output GCF_018617855.1_ASM1861785v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:34:34,830] [INFO] Task succeeded: fastANI
[2024-01-24 12:34:34,831] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb6387e4c-cd7b-4e66-a8f2-670e79c34161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:34:34,832] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb6387e4c-cd7b-4e66-a8f2-670e79c34161/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:34:34,905] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:34:34,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:34:34,906] [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 qingdaonense	strain=S82	GCA_018617855.1	2751251	2751251	type	True	100.0	892	893	95	conclusive
Exiguobacterium marinum	strain=DSM 16307	GCA_000620845.1	273528	273528	type	True	87.201	788	893	95	below_threshold
Exiguobacterium profundum	strain=10C	GCA_025234635.1	307643	307643	type	True	87.0039	732	893	95	below_threshold
Exiguobacterium aestuarii	strain=TF_16	GCA_025234735.1	273527	273527	type	True	86.1976	674	893	95	below_threshold
Exiguobacterium algae	strain=S126	GCA_018617875.1	2751250	2751250	type	True	82.6854	560	893	95	below_threshold
Exiguobacterium chiriqhucha	strain=RW-2	GCA_000416965.1	1385984	1385984	type	True	80.8449	534	893	95	below_threshold
Exiguobacterium himgiriensis	strain=K22_26	GCA_025234715.1	384621	384621	type	True	80.5215	478	893	95	below_threshold
Exiguobacterium undae	strain=DSM 14481	GCA_000620805.1	169177	169177	type	True	77.4656	118	893	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:34:34,907] [INFO] DFAST Taxonomy check result was written to GCF_018617855.1_ASM1861785v1_genomic.fna/tc_result.tsv
[2024-01-24 12:34:34,908] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:34:34,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:34:34,909] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb6387e4c-cd7b-4e66-a8f2-670e79c34161/dqc_reference/checkm_data
[2024-01-24 12:34:34,914] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:34:34,941] [INFO] Task started: CheckM
[2024-01-24 12:34:34,941] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_018617855.1_ASM1861785v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_018617855.1_ASM1861785v1_genomic.fna/checkm_input GCF_018617855.1_ASM1861785v1_genomic.fna/checkm_result
[2024-01-24 12:35:04,285] [INFO] Task succeeded: CheckM
[2024-01-24 12:35:04,287] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:35:04,303] [INFO] ===== Completeness check finished =====
[2024-01-24 12:35:04,303] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:35:04,304] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_018617855.1_ASM1861785v1_genomic.fna/markers.fasta)
[2024-01-24 12:35:04,304] [INFO] Task started: Blastn
[2024-01-24 12:35:04,305] [INFO] Running command: blastn -query GCF_018617855.1_ASM1861785v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb6387e4c-cd7b-4e66-a8f2-670e79c34161/dqc_reference/reference_markers_gtdb.fasta -out GCF_018617855.1_ASM1861785v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:35:05,071] [INFO] Task succeeded: Blastn
[2024-01-24 12:35:05,075] [INFO] Selected 7 target genomes.
[2024-01-24 12:35:05,075] [INFO] Target genome list was writen to GCF_018617855.1_ASM1861785v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:35:05,080] [INFO] Task started: fastANI
[2024-01-24 12:35:05,081] [INFO] Running command: fastANI --query /var/lib/cwl/stgccc7a0c0-2527-4bb6-9e56-8be58207156b/GCF_018617855.1_ASM1861785v1_genomic.fna.gz --refList GCF_018617855.1_ASM1861785v1_genomic.fna/target_genomes_gtdb.txt --output GCF_018617855.1_ASM1861785v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:35:09,907] [INFO] Task succeeded: fastANI
[2024-01-24 12:35:09,923] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:35:09,923] [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_018617855.1	s__Exiguobacterium sp018617855	100.0	892	893	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_000620845.1	s__Exiguobacterium marinum	87.201	788	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	98.37	97.95	0.94	0.94	10	-
GCF_001909285.1	s__Exiguobacterium profundum_A	87.051	789	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.55	95.32	0.92	0.88	29	-
GCA_902362975.1	s__Exiguobacterium sp902362975	86.7625	717	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.52	95.12	0.85	0.82	3	-
GCF_018617395.1	s__Exiguobacterium sp018617395	86.6412	761	893	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	86.3639	737	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	95.57	95.32	0.91	0.90	6	-
GCF_018617485.1	s__Exiguobacterium sp018617485	86.1674	757	893	d__Bacteria;p__Firmicutes;c__Bacilli;o__Exiguobacterales;f__Exiguobacteraceae;g__Exiguobacterium	95.0	96.75	95.34	0.91	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:35:09,925] [INFO] GTDB search result was written to GCF_018617855.1_ASM1861785v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:35:09,925] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:35:09,928] [INFO] DFAST_QC result json was written to GCF_018617855.1_ASM1861785v1_genomic.fna/dqc_result.json
[2024-01-24 12:35:09,928] [INFO] DFAST_QC completed!
[2024-01-24 12:35:09,928] [INFO] Total running time: 0h0m50s