[2024-01-25 20:19:20,622] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:19:20,630] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:19:20,631] [INFO] DQC Reference Directory: /var/lib/cwl/stg42493e85-bd42-43ef-82ad-90e51c289662/dqc_reference
[2024-01-25 20:19:21,758] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:19:21,761] [INFO] Task started: Prodigal
[2024-01-25 20:19:21,761] [INFO] Running command: gunzip -c /var/lib/cwl/stga4e5b4e7-7e18-4638-bfb9-9c065a591cc9/GCF_000263195.1_ASM26319v1_genomic.fna.gz | prodigal -d GCF_000263195.1_ASM26319v1_genomic.fna/cds.fna -a GCF_000263195.1_ASM26319v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:19:38,410] [INFO] Task succeeded: Prodigal
[2024-01-25 20:19:38,410] [INFO] Task started: HMMsearch
[2024-01-25 20:19:38,410] [INFO] Running command: hmmsearch --tblout GCF_000263195.1_ASM26319v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg42493e85-bd42-43ef-82ad-90e51c289662/dqc_reference/reference_markers.hmm GCF_000263195.1_ASM26319v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:19:38,722] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:19:38,723] [INFO] Found 6/6 markers.
[2024-01-25 20:19:38,768] [INFO] Query marker FASTA was written to GCF_000263195.1_ASM26319v1_genomic.fna/markers.fasta
[2024-01-25 20:19:38,769] [INFO] Task started: Blastn
[2024-01-25 20:19:38,769] [INFO] Running command: blastn -query GCF_000263195.1_ASM26319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42493e85-bd42-43ef-82ad-90e51c289662/dqc_reference/reference_markers.fasta -out GCF_000263195.1_ASM26319v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:19:39,320] [INFO] Task succeeded: Blastn
[2024-01-25 20:19:39,322] [INFO] Selected 15 target genomes.
[2024-01-25 20:19:39,323] [INFO] Target genome list was writen to GCF_000263195.1_ASM26319v1_genomic.fna/target_genomes.txt
[2024-01-25 20:19:39,335] [INFO] Task started: fastANI
[2024-01-25 20:19:39,335] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e5b4e7-7e18-4638-bfb9-9c065a591cc9/GCF_000263195.1_ASM26319v1_genomic.fna.gz --refList GCF_000263195.1_ASM26319v1_genomic.fna/target_genomes.txt --output GCF_000263195.1_ASM26319v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:19:50,981] [INFO] Task succeeded: fastANI
[2024-01-25 20:19:50,982] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg42493e85-bd42-43ef-82ad-90e51c289662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:19:50,982] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg42493e85-bd42-43ef-82ad-90e51c289662/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:19:50,988] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:19:50,988] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:19:50,988] [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
Emticicia aquatilis	strain=CGMCC 1.15958	GCA_014644295.1	1537369	1537369	type	True	80.2757	1054	1737	95	below_threshold
Emticicia aquatica	strain=CECT 8858, type strain	GCA_923079645.1	1681835	1681835	type	True	78.4934	772	1737	95	below_threshold
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	76.8022	257	1737	95	below_threshold
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	76.2299	112	1737	95	below_threshold
Dyadobacter subterraneus	strain=UP-52	GCA_015221875.1	2773304	2773304	type	True	75.8698	63	1737	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:19:50,990] [INFO] DFAST Taxonomy check result was written to GCF_000263195.1_ASM26319v1_genomic.fna/tc_result.tsv
[2024-01-25 20:19:50,990] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:19:50,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:19:50,990] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg42493e85-bd42-43ef-82ad-90e51c289662/dqc_reference/checkm_data
[2024-01-25 20:19:50,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:19:51,046] [INFO] Task started: CheckM
[2024-01-25 20:19:51,046] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000263195.1_ASM26319v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000263195.1_ASM26319v1_genomic.fna/checkm_input GCF_000263195.1_ASM26319v1_genomic.fna/checkm_result
[2024-01-25 20:20:40,460] [INFO] Task succeeded: CheckM
[2024-01-25 20:20:40,461] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:20:40,477] [INFO] ===== Completeness check finished =====
[2024-01-25 20:20:40,478] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:20:40,478] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000263195.1_ASM26319v1_genomic.fna/markers.fasta)
[2024-01-25 20:20:40,479] [INFO] Task started: Blastn
[2024-01-25 20:20:40,479] [INFO] Running command: blastn -query GCF_000263195.1_ASM26319v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg42493e85-bd42-43ef-82ad-90e51c289662/dqc_reference/reference_markers_gtdb.fasta -out GCF_000263195.1_ASM26319v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:20:41,248] [INFO] Task succeeded: Blastn
[2024-01-25 20:20:41,251] [INFO] Selected 16 target genomes.
[2024-01-25 20:20:41,251] [INFO] Target genome list was writen to GCF_000263195.1_ASM26319v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:20:41,274] [INFO] Task started: fastANI
[2024-01-25 20:20:41,274] [INFO] Running command: fastANI --query /var/lib/cwl/stga4e5b4e7-7e18-4638-bfb9-9c065a591cc9/GCF_000263195.1_ASM26319v1_genomic.fna.gz --refList GCF_000263195.1_ASM26319v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000263195.1_ASM26319v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:20:54,954] [INFO] Task succeeded: fastANI
[2024-01-25 20:20:54,960] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:20:54,960] [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
GCA_000263195.1	s__Emticicia oligotrophica	100.0	1736	1737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014644295.1	s__Emticicia aquatilis	80.2736	1054	1737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017495105.1	s__Emticicia sp017495105	79.1986	726	1737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168285.1	s__Emticicia sp004168285	76.7936	258	1737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013912375.1	s__Emticicia sp013912375	76.6303	260	1737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003418935.1	s__Emticicia sp003418935	76.4518	281	1737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013298865.1	s__JAAFJL01 sp013298865	75.4235	75	1737	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__JAAFJL01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:20:54,963] [INFO] GTDB search result was written to GCF_000263195.1_ASM26319v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:20:54,963] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:20:54,966] [INFO] DFAST_QC result json was written to GCF_000263195.1_ASM26319v1_genomic.fna/dqc_result.json
[2024-01-25 20:20:54,966] [INFO] DFAST_QC completed!
[2024-01-25 20:20:54,966] [INFO] Total running time: 0h1m34s