[2024-01-24 12:06:14,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,166] [INFO] DQC Reference Directory: /var/lib/cwl/stgbed2e355-ec3c-4ed4-a994-a09112ab443c/dqc_reference
[2024-01-24 12:06:15,526] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,527] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,527] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d8ef211-cf6b-46bb-b2b1-6b3d5bcc7354/GCF_023701865.1_ASM2370186v1_genomic.fna.gz | prodigal -d GCF_023701865.1_ASM2370186v1_genomic.fna/cds.fna -a GCF_023701865.1_ASM2370186v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:18,896] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:18,897] [INFO] Task started: HMMsearch
[2024-01-24 12:06:18,897] [INFO] Running command: hmmsearch --tblout GCF_023701865.1_ASM2370186v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbed2e355-ec3c-4ed4-a994-a09112ab443c/dqc_reference/reference_markers.hmm GCF_023701865.1_ASM2370186v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:19,202] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:19,203] [INFO] Found 6/6 markers.
[2024-01-24 12:06:19,235] [INFO] Query marker FASTA was written to GCF_023701865.1_ASM2370186v1_genomic.fna/markers.fasta
[2024-01-24 12:06:19,236] [INFO] Task started: Blastn
[2024-01-24 12:06:19,236] [INFO] Running command: blastn -query GCF_023701865.1_ASM2370186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbed2e355-ec3c-4ed4-a994-a09112ab443c/dqc_reference/reference_markers.fasta -out GCF_023701865.1_ASM2370186v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:20,272] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:20,275] [INFO] Selected 20 target genomes.
[2024-01-24 12:06:20,276] [INFO] Target genome list was writen to GCF_023701865.1_ASM2370186v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:21,765] [INFO] Task started: fastANI
[2024-01-24 12:06:21,766] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8ef211-cf6b-46bb-b2b1-6b3d5bcc7354/GCF_023701865.1_ASM2370186v1_genomic.fna.gz --refList GCF_023701865.1_ASM2370186v1_genomic.fna/target_genomes.txt --output GCF_023701865.1_ASM2370186v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:27,833] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:27,834] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbed2e355-ec3c-4ed4-a994-a09112ab443c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:27,834] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbed2e355-ec3c-4ed4-a994-a09112ab443c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:27,847] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:06:27,853] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:27,853] [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
Periweissella beninensis	strain=LMG 25373	GCA_023701865.1	504936	504936	type	True	100.0	568	571	95	conclusive
Periweissella beninensis	strain=DSM 22752	GCA_016908275.1	504936	504936	type	True	99.9279	566	571	95	conclusive
Periweissella fabalis	strain=LMG 26217	GCA_023657345.1	1070421	1070421	type	True	78.6036	136	571	95	below_threshold
Periweissella ghanensis	strain=LMG 24286 substr. LMG 24286	GCA_918814755.1	467997	467997	type	True	78.5947	108	571	95	below_threshold
Periweissella fabaria	strain=LMG 24289 substr. LMG 24289	GCA_918814575.1	546157	546157	type	True	78.4708	137	571	95	below_threshold
Periweissella ghanensis	strain=DSM 19935	GCA_023657365.1	467997	467997	type	True	78.4652	110	571	95	below_threshold
Periweissella fabaria	strain=LMG 24289	GCA_023657385.1	546157	546157	type	True	78.4603	130	571	95	below_threshold
Periweissella fabalis	strain=CCUG 61472	GCA_012396505.1	1070421	1070421	type	True	78.325	140	571	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:27,856] [INFO] DFAST Taxonomy check result was written to GCF_023701865.1_ASM2370186v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:27,858] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:27,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:27,859] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbed2e355-ec3c-4ed4-a994-a09112ab443c/dqc_reference/checkm_data
[2024-01-24 12:06:27,860] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:27,885] [INFO] Task started: CheckM
[2024-01-24 12:06:27,886] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023701865.1_ASM2370186v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023701865.1_ASM2370186v1_genomic.fna/checkm_input GCF_023701865.1_ASM2370186v1_genomic.fna/checkm_result
[2024-01-24 12:06:46,807] [INFO] Task succeeded: CheckM
[2024-01-24 12:06:46,809] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:06:46,831] [INFO] ===== Completeness check finished =====
[2024-01-24 12:06:46,832] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:06:46,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023701865.1_ASM2370186v1_genomic.fna/markers.fasta)
[2024-01-24 12:06:46,833] [INFO] Task started: Blastn
[2024-01-24 12:06:46,833] [INFO] Running command: blastn -query GCF_023701865.1_ASM2370186v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbed2e355-ec3c-4ed4-a994-a09112ab443c/dqc_reference/reference_markers_gtdb.fasta -out GCF_023701865.1_ASM2370186v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:47,683] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:47,687] [INFO] Selected 26 target genomes.
[2024-01-24 12:06:47,687] [INFO] Target genome list was writen to GCF_023701865.1_ASM2370186v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:06:47,713] [INFO] Task started: fastANI
[2024-01-24 12:06:47,713] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d8ef211-cf6b-46bb-b2b1-6b3d5bcc7354/GCF_023701865.1_ASM2370186v1_genomic.fna.gz --refList GCF_023701865.1_ASM2370186v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023701865.1_ASM2370186v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:06:56,616] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:56,621] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:06:56,621] [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_016908275.1	s__Weissella_A beninensis	99.9279	566	571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004358325.1	s__Weissella_A cryptocerci	78.3687	74	571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396505.1	s__Weissella_A fabalis	78.3374	139	571	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:06:56,624] [INFO] GTDB search result was written to GCF_023701865.1_ASM2370186v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:06:56,625] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:06:56,633] [INFO] DFAST_QC result json was written to GCF_023701865.1_ASM2370186v1_genomic.fna/dqc_result.json
[2024-01-24 12:06:56,633] [INFO] DFAST_QC completed!
[2024-01-24 12:06:56,634] [INFO] Total running time: 0h0m42s