[2024-01-24 12:28:35,045] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:35,046] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:35,046] [INFO] DQC Reference Directory: /var/lib/cwl/stg4118c3d8-038a-4c33-a3f7-29fa00524a3a/dqc_reference
[2024-01-24 12:28:36,252] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:36,253] [INFO] Task started: Prodigal
[2024-01-24 12:28:36,253] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cc6af7d-4822-4773-bd11-79350647b639/GCF_006540065.1_ASM654006v1_genomic.fna.gz | prodigal -d GCF_006540065.1_ASM654006v1_genomic.fna/cds.fna -a GCF_006540065.1_ASM654006v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:39,993] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:39,994] [INFO] Task started: HMMsearch
[2024-01-24 12:28:39,994] [INFO] Running command: hmmsearch --tblout GCF_006540065.1_ASM654006v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4118c3d8-038a-4c33-a3f7-29fa00524a3a/dqc_reference/reference_markers.hmm GCF_006540065.1_ASM654006v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:40,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:40,222] [INFO] Found 6/6 markers.
[2024-01-24 12:28:40,244] [INFO] Query marker FASTA was written to GCF_006540065.1_ASM654006v1_genomic.fna/markers.fasta
[2024-01-24 12:28:40,244] [INFO] Task started: Blastn
[2024-01-24 12:28:40,244] [INFO] Running command: blastn -query GCF_006540065.1_ASM654006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4118c3d8-038a-4c33-a3f7-29fa00524a3a/dqc_reference/reference_markers.fasta -out GCF_006540065.1_ASM654006v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:40,817] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:40,821] [INFO] Selected 10 target genomes.
[2024-01-24 12:28:40,821] [INFO] Target genome list was writen to GCF_006540065.1_ASM654006v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:40,901] [INFO] Task started: fastANI
[2024-01-24 12:28:40,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc6af7d-4822-4773-bd11-79350647b639/GCF_006540065.1_ASM654006v1_genomic.fna.gz --refList GCF_006540065.1_ASM654006v1_genomic.fna/target_genomes.txt --output GCF_006540065.1_ASM654006v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:44,203] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:44,204] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4118c3d8-038a-4c33-a3f7-29fa00524a3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:44,204] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4118c3d8-038a-4c33-a3f7-29fa00524a3a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:44,213] [INFO] Found 6 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:28:44,213] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:28:44,213] [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
Weissella hellenica	strain=NBRC 15553	GCA_006540065.1	46256	46256	suspected-type	True	100.0	580	581	95	conclusive
Weissella hellenica	strain=CCUG 33494	GCA_012396435.1	46256	46256	suspected-type	True	99.9997	580	581	95	conclusive
Weissella hellenica	strain=NBRC 15553	GCA_005405545.1	46256	46256	suspected-type	True	99.9959	578	581	95	conclusive
Weissella sagaensis	strain=X0750	GCA_005405285.1	2559928	2559928	type	True	90.4213	509	581	95	below_threshold
Weissella bombi	strain=DSM 28794	GCA_005405505.1	1505725	1505725	type	True	85.7253	459	581	95	below_threshold
Weissella bombi	strain=R-53094	GCA_900094835.1	1505725	1505725	type	True	85.6627	469	581	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:44,215] [INFO] DFAST Taxonomy check result was written to GCF_006540065.1_ASM654006v1_genomic.fna/tc_result.tsv
[2024-01-24 12:28:44,216] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:44,217] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:44,217] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4118c3d8-038a-4c33-a3f7-29fa00524a3a/dqc_reference/checkm_data
[2024-01-24 12:28:44,219] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:44,244] [INFO] Task started: CheckM
[2024-01-24 12:28:44,244] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006540065.1_ASM654006v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006540065.1_ASM654006v1_genomic.fna/checkm_input GCF_006540065.1_ASM654006v1_genomic.fna/checkm_result
[2024-01-24 12:29:02,603] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:02,605] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:02,624] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:02,625] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:02,625] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006540065.1_ASM654006v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:02,625] [INFO] Task started: Blastn
[2024-01-24 12:29:02,626] [INFO] Running command: blastn -query GCF_006540065.1_ASM654006v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4118c3d8-038a-4c33-a3f7-29fa00524a3a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006540065.1_ASM654006v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:03,392] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:03,395] [INFO] Selected 11 target genomes.
[2024-01-24 12:29:03,395] [INFO] Target genome list was writen to GCF_006540065.1_ASM654006v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:03,425] [INFO] Task started: fastANI
[2024-01-24 12:29:03,425] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cc6af7d-4822-4773-bd11-79350647b639/GCF_006540065.1_ASM654006v1_genomic.fna.gz --refList GCF_006540065.1_ASM654006v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006540065.1_ASM654006v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:07,724] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:07,740] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:29:07,740] [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_005405545.1	s__Weissella hellenica	99.9959	578	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	99.99	0.99	0.99	4	conclusive
GCF_006777025.1	s__Weissella hellenica_B	90.3678	495	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.22	98.80	0.93	0.90	9	-
GCF_900094835.1	s__Weissella bombi	85.6868	468	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000160575.1	s__Weissella paramesenteroides	80.5393	321	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.27	97.99	0.88	0.85	25	-
GCF_005405465.1	s__Weissella thailandensis	80.4901	321	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.06	96.27	0.98	0.95	5	-
GCF_004771295.1	s__Weissella confusa_B	78.7479	105	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.67	96.65	0.95	0.87	5	-
GCA_001436895.1	s__Weissella confusa	78.5821	110	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_004521965.1	s__Weissella cibaria_A	78.4498	106	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003862435.1	s__Weissella viridescens_A	78.2391	84	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001437425.1	s__Weissella minor	78.1044	102	581	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:07,742] [INFO] GTDB search result was written to GCF_006540065.1_ASM654006v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:07,742] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:07,745] [INFO] DFAST_QC result json was written to GCF_006540065.1_ASM654006v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:07,745] [INFO] DFAST_QC completed!
[2024-01-24 12:29:07,746] [INFO] Total running time: 0h0m33s