[2024-01-24 12:13:06,372] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:06,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:06,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgd06ba838-a55d-4df0-ae40-ecbe005191d2/dqc_reference
[2024-01-24 12:13:07,529] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:07,530] [INFO] Task started: Prodigal
[2024-01-24 12:13:07,530] [INFO] Running command: gunzip -c /var/lib/cwl/stg0fc4126e-c7fa-4a2f-8ea7-022e32f4dffe/GCF_005405285.1_ASM540528v1_genomic.fna.gz | prodigal -d GCF_005405285.1_ASM540528v1_genomic.fna/cds.fna -a GCF_005405285.1_ASM540528v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:11,515] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:11,516] [INFO] Task started: HMMsearch
[2024-01-24 12:13:11,516] [INFO] Running command: hmmsearch --tblout GCF_005405285.1_ASM540528v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd06ba838-a55d-4df0-ae40-ecbe005191d2/dqc_reference/reference_markers.hmm GCF_005405285.1_ASM540528v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:11,689] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:11,690] [INFO] Found 6/6 markers.
[2024-01-24 12:13:11,711] [INFO] Query marker FASTA was written to GCF_005405285.1_ASM540528v1_genomic.fna/markers.fasta
[2024-01-24 12:13:11,711] [INFO] Task started: Blastn
[2024-01-24 12:13:11,711] [INFO] Running command: blastn -query GCF_005405285.1_ASM540528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd06ba838-a55d-4df0-ae40-ecbe005191d2/dqc_reference/reference_markers.fasta -out GCF_005405285.1_ASM540528v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:12,255] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:12,258] [INFO] Selected 9 target genomes.
[2024-01-24 12:13:12,258] [INFO] Target genome list was writen to GCF_005405285.1_ASM540528v1_genomic.fna/target_genomes.txt
[2024-01-24 12:13:12,280] [INFO] Task started: fastANI
[2024-01-24 12:13:12,280] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc4126e-c7fa-4a2f-8ea7-022e32f4dffe/GCF_005405285.1_ASM540528v1_genomic.fna.gz --refList GCF_005405285.1_ASM540528v1_genomic.fna/target_genomes.txt --output GCF_005405285.1_ASM540528v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:15,348] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:15,348] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd06ba838-a55d-4df0-ae40-ecbe005191d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:15,349] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd06ba838-a55d-4df0-ae40-ecbe005191d2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:15,355] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:15,356] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:15,356] [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 sagaensis	strain=X0750	GCA_005405285.1	2559928	2559928	type	True	100.0	633	634	95	conclusive
Weissella hellenica	strain=NBRC 15553	GCA_005405545.1	46256	46256	suspected-type	True	90.4019	509	634	95	below_threshold
Weissella hellenica	strain=CCUG 33494	GCA_012396435.1	46256	46256	suspected-type	True	90.3957	523	634	95	below_threshold
Weissella hellenica	strain=NBRC 15553	GCA_006540065.1	46256	46256	suspected-type	True	90.2723	513	634	95	below_threshold
Weissella bombi	strain=R-53094	GCA_900094835.1	1505725	1505725	type	True	85.3204	448	634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:15,357] [INFO] DFAST Taxonomy check result was written to GCF_005405285.1_ASM540528v1_genomic.fna/tc_result.tsv
[2024-01-24 12:13:15,361] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:15,362] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:15,362] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd06ba838-a55d-4df0-ae40-ecbe005191d2/dqc_reference/checkm_data
[2024-01-24 12:13:15,363] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:15,383] [INFO] Task started: CheckM
[2024-01-24 12:13:15,383] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405285.1_ASM540528v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405285.1_ASM540528v1_genomic.fna/checkm_input GCF_005405285.1_ASM540528v1_genomic.fna/checkm_result
[2024-01-24 12:13:35,195] [INFO] Task succeeded: CheckM
[2024-01-24 12:13:35,197] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:13:35,211] [INFO] ===== Completeness check finished =====
[2024-01-24 12:13:35,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:13:35,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405285.1_ASM540528v1_genomic.fna/markers.fasta)
[2024-01-24 12:13:35,212] [INFO] Task started: Blastn
[2024-01-24 12:13:35,213] [INFO] Running command: blastn -query GCF_005405285.1_ASM540528v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd06ba838-a55d-4df0-ae40-ecbe005191d2/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405285.1_ASM540528v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:35,937] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:35,941] [INFO] Selected 8 target genomes.
[2024-01-24 12:13:35,941] [INFO] Target genome list was writen to GCF_005405285.1_ASM540528v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:13:35,949] [INFO] Task started: fastANI
[2024-01-24 12:13:35,950] [INFO] Running command: fastANI --query /var/lib/cwl/stg0fc4126e-c7fa-4a2f-8ea7-022e32f4dffe/GCF_005405285.1_ASM540528v1_genomic.fna.gz --refList GCF_005405285.1_ASM540528v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405285.1_ASM540528v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:13:39,144] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:39,153] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:13:39,153] [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_006777025.1	s__Weissella hellenica_B	99.3071	592	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.22	98.80	0.93	0.90	9	conclusive
GCF_005405545.1	s__Weissella hellenica	90.434	508	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	99.99	0.99	0.99	4	-
GCF_900094835.1	s__Weissella bombi	85.3166	448	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_005405465.1	s__Weissella thailandensis	80.8776	344	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.06	96.27	0.98	0.95	5	-
GCF_000160575.1	s__Weissella paramesenteroides	80.7426	331	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.27	97.99	0.88	0.85	25	-
GCF_000277645.1	s__Weissella koreensis	79.1975	71	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.29	98.85	0.93	0.91	5	-
GCF_004521965.1	s__Weissella cibaria_A	78.931	118	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:13:39,216] [INFO] GTDB search result was written to GCF_005405285.1_ASM540528v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:13:39,216] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:13:39,219] [INFO] DFAST_QC result json was written to GCF_005405285.1_ASM540528v1_genomic.fna/dqc_result.json
[2024-01-24 12:13:39,219] [INFO] DFAST_QC completed!
[2024-01-24 12:13:39,219] [INFO] Total running time: 0h0m33s