[2024-01-24 12:21:57,646] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:57,648] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:57,648] [INFO] DQC Reference Directory: /var/lib/cwl/stg557f51fc-dffe-4b37-9e4b-493f8e507bda/dqc_reference
[2024-01-24 12:21:59,028] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:59,028] [INFO] Task started: Prodigal
[2024-01-24 12:21:59,029] [INFO] Running command: gunzip -c /var/lib/cwl/stg487e58fe-5bde-49ed-8538-68b1f6265a40/GCF_009764365.1_L._kimchii_genomic.fna.gz | prodigal -d GCF_009764365.1_L._kimchii_genomic.fna/cds.fna -a GCF_009764365.1_L._kimchii_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:22:05,653] [INFO] Task succeeded: Prodigal
[2024-01-24 12:22:05,654] [INFO] Task started: HMMsearch
[2024-01-24 12:22:05,654] [INFO] Running command: hmmsearch --tblout GCF_009764365.1_L._kimchii_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg557f51fc-dffe-4b37-9e4b-493f8e507bda/dqc_reference/reference_markers.hmm GCF_009764365.1_L._kimchii_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:05,930] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:05,932] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg487e58fe-5bde-49ed-8538-68b1f6265a40/GCF_009764365.1_L._kimchii_genomic.fna.gz]
[2024-01-24 12:22:05,962] [INFO] Query marker FASTA was written to GCF_009764365.1_L._kimchii_genomic.fna/markers.fasta
[2024-01-24 12:22:05,963] [INFO] Task started: Blastn
[2024-01-24 12:22:05,963] [INFO] Running command: blastn -query GCF_009764365.1_L._kimchii_genomic.fna/markers.fasta -db /var/lib/cwl/stg557f51fc-dffe-4b37-9e4b-493f8e507bda/dqc_reference/reference_markers.fasta -out GCF_009764365.1_L._kimchii_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:06,535] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:06,538] [INFO] Selected 10 target genomes.
[2024-01-24 12:22:06,538] [INFO] Target genome list was writen to GCF_009764365.1_L._kimchii_genomic.fna/target_genomes.txt
[2024-01-24 12:22:06,541] [INFO] Task started: fastANI
[2024-01-24 12:22:06,541] [INFO] Running command: fastANI --query /var/lib/cwl/stg487e58fe-5bde-49ed-8538-68b1f6265a40/GCF_009764365.1_L._kimchii_genomic.fna.gz --refList GCF_009764365.1_L._kimchii_genomic.fna/target_genomes.txt --output GCF_009764365.1_L._kimchii_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:13,565] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:13,566] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg557f51fc-dffe-4b37-9e4b-493f8e507bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:13,566] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg557f51fc-dffe-4b37-9e4b-493f8e507bda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:13,577] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:22:13,577] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:13,578] [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
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	100.0	985	1051	95	conclusive
Companilactobacillus kimchii	strain=DSM 13961	GCA_001435445.1	2801452	2801452	type	True	99.9856	897	1051	95	conclusive
Companilactobacillus kimchii	strain=JCM 10707	GCA_001311095.1	2801452	2801452	type	True	99.948	896	1051	95	conclusive
Companilactobacillus bobalius	strain=DSM 19674	GCA_001434855.1	2801451	2801451	type	True	92.3446	787	1051	95	below_threshold
Companilactobacillus bobalius	strain=203	GCA_009764355.1	2801451	2801451	type	True	92.2577	825	1051	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_001434985.1	83526	83526	type	True	92.003	684	1051	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	91.983	703	1051	95	below_threshold
Companilactobacillus allii	strain=WiKim39	GCA_023923085.1	1847728	1847728	type	True	79.8021	286	1051	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	79.2491	188	1051	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:13,585] [INFO] DFAST Taxonomy check result was written to GCF_009764365.1_L._kimchii_genomic.fna/tc_result.tsv
[2024-01-24 12:22:13,586] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:13,586] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:13,587] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg557f51fc-dffe-4b37-9e4b-493f8e507bda/dqc_reference/checkm_data
[2024-01-24 12:22:13,588] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:13,620] [INFO] Task started: CheckM
[2024-01-24 12:22:13,620] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009764365.1_L._kimchii_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009764365.1_L._kimchii_genomic.fna/checkm_input GCF_009764365.1_L._kimchii_genomic.fna/checkm_result
[2024-01-24 12:22:38,937] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:38,938] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:38,957] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:38,957] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:38,958] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009764365.1_L._kimchii_genomic.fna/markers.fasta)
[2024-01-24 12:22:38,958] [INFO] Task started: Blastn
[2024-01-24 12:22:38,958] [INFO] Running command: blastn -query GCF_009764365.1_L._kimchii_genomic.fna/markers.fasta -db /var/lib/cwl/stg557f51fc-dffe-4b37-9e4b-493f8e507bda/dqc_reference/reference_markers_gtdb.fasta -out GCF_009764365.1_L._kimchii_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:39,727] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:39,730] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:39,731] [INFO] Target genome list was writen to GCF_009764365.1_L._kimchii_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:39,734] [INFO] Task started: fastANI
[2024-01-24 12:22:39,734] [INFO] Running command: fastANI --query /var/lib/cwl/stg487e58fe-5bde-49ed-8538-68b1f6265a40/GCF_009764365.1_L._kimchii_genomic.fna.gz --refList GCF_009764365.1_L._kimchii_genomic.fna/target_genomes_gtdb.txt --output GCF_009764365.1_L._kimchii_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:45,954] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:45,962] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:45,963] [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_001435445.1	s__Companilactobacillus kimchii	99.9856	897	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.97	1.00	1.00	5	conclusive
GCF_009764355.1	s__Companilactobacillus paralimentarius_A	92.2786	818	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.92	99.92	1.00	0.99	4	-
GCF_001434985.1	s__Companilactobacillus paralimentarius	92.0123	683	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.97	99.96	0.99	0.99	4	-
GCA_019116025.1	s__Companilactobacillus pullicola	86.7838	699	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002849895.1	s__Companilactobacillus alimentarius	83.0947	517	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	99.99	1.00	1.00	3	-
GCF_004745525.1	s__Companilactobacillus suantsaicola	82.6873	488	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003967595.1	s__Companilactobacillus musae	82.4399	455	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002706745.1	s__Companilactobacillus farciminis	81.902	435	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	98.95	96.63	0.97	0.92	6	-
GCF_001435815.1	s__Companilactobacillus nantensis	81.6616	445	1051	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:45,965] [INFO] GTDB search result was written to GCF_009764365.1_L._kimchii_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:45,966] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:45,968] [INFO] DFAST_QC result json was written to GCF_009764365.1_L._kimchii_genomic.fna/dqc_result.json
[2024-01-24 12:22:45,969] [INFO] DFAST_QC completed!
[2024-01-24 12:22:45,969] [INFO] Total running time: 0h0m48s