[2024-01-24 12:13:56,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:56,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:56,712] [INFO] DQC Reference Directory: /var/lib/cwl/stg07ebb48f-02c0-4a03-8629-58661c7e41e2/dqc_reference
[2024-01-24 12:13:57,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:57,945] [INFO] Task started: Prodigal
[2024-01-24 12:13:57,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ad4d7c3-487b-4888-a29a-293d94bc415e/GCF_000177375.1_ASM17737v1_genomic.fna.gz | prodigal -d GCF_000177375.1_ASM17737v1_genomic.fna/cds.fna -a GCF_000177375.1_ASM17737v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:14:01,100] [INFO] Task succeeded: Prodigal
[2024-01-24 12:14:01,100] [INFO] Task started: HMMsearch
[2024-01-24 12:14:01,101] [INFO] Running command: hmmsearch --tblout GCF_000177375.1_ASM17737v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg07ebb48f-02c0-4a03-8629-58661c7e41e2/dqc_reference/reference_markers.hmm GCF_000177375.1_ASM17737v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:14:01,488] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:14:01,489] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg0ad4d7c3-487b-4888-a29a-293d94bc415e/GCF_000177375.1_ASM17737v1_genomic.fna.gz]
[2024-01-24 12:14:01,506] [INFO] Query marker FASTA was written to GCF_000177375.1_ASM17737v1_genomic.fna/markers.fasta
[2024-01-24 12:14:01,510] [INFO] Task started: Blastn
[2024-01-24 12:14:01,510] [INFO] Running command: blastn -query GCF_000177375.1_ASM17737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07ebb48f-02c0-4a03-8629-58661c7e41e2/dqc_reference/reference_markers.fasta -out GCF_000177375.1_ASM17737v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:04,288] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:04,292] [INFO] Selected 15 target genomes.
[2024-01-24 12:14:04,292] [INFO] Target genome list was writen to GCF_000177375.1_ASM17737v1_genomic.fna/target_genomes.txt
[2024-01-24 12:14:04,431] [INFO] Task started: fastANI
[2024-01-24 12:14:04,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad4d7c3-487b-4888-a29a-293d94bc415e/GCF_000177375.1_ASM17737v1_genomic.fna.gz --refList GCF_000177375.1_ASM17737v1_genomic.fna/target_genomes.txt --output GCF_000177375.1_ASM17737v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:14:10,807] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:10,808] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg07ebb48f-02c0-4a03-8629-58661c7e41e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:14:10,808] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg07ebb48f-02c0-4a03-8629-58661c7e41e2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:14:10,811] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:14:10,811] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:14:10,811] [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
Bulleidia extructa	strain=W1219	GCA_000177375.1	118748	118748	type	True	100.0	465	466	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:14:10,813] [INFO] DFAST Taxonomy check result was written to GCF_000177375.1_ASM17737v1_genomic.fna/tc_result.tsv
[2024-01-24 12:14:10,814] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:14:10,814] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:14:10,814] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg07ebb48f-02c0-4a03-8629-58661c7e41e2/dqc_reference/checkm_data
[2024-01-24 12:14:10,815] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:14:10,833] [INFO] Task started: CheckM
[2024-01-24 12:14:10,833] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000177375.1_ASM17737v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000177375.1_ASM17737v1_genomic.fna/checkm_input GCF_000177375.1_ASM17737v1_genomic.fna/checkm_result
[2024-01-24 12:14:29,135] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:29,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:29,158] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:29,158] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:29,158] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000177375.1_ASM17737v1_genomic.fna/markers.fasta)
[2024-01-24 12:14:29,159] [INFO] Task started: Blastn
[2024-01-24 12:14:29,159] [INFO] Running command: blastn -query GCF_000177375.1_ASM17737v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg07ebb48f-02c0-4a03-8629-58661c7e41e2/dqc_reference/reference_markers_gtdb.fasta -out GCF_000177375.1_ASM17737v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:29,982] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:29,986] [INFO] Selected 17 target genomes.
[2024-01-24 12:14:29,986] [INFO] Target genome list was writen to GCF_000177375.1_ASM17737v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:30,033] [INFO] Task started: fastANI
[2024-01-24 12:14:30,034] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ad4d7c3-487b-4888-a29a-293d94bc415e/GCF_000177375.1_ASM17737v1_genomic.fna.gz --refList GCF_000177375.1_ASM17737v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000177375.1_ASM17737v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:36,856] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:36,862] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:36,863] [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_000177375.1	s__Bulleidia extructa	100.0	465	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	98.85	98.85	0.97	0.97	2	conclusive
GCF_016812035.1	s__Bulleidia sp016812035	80.454	279	466	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:36,867] [INFO] GTDB search result was written to GCF_000177375.1_ASM17737v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:36,868] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:36,871] [INFO] DFAST_QC result json was written to GCF_000177375.1_ASM17737v1_genomic.fna/dqc_result.json
[2024-01-24 12:14:36,871] [INFO] DFAST_QC completed!
[2024-01-24 12:14:36,871] [INFO] Total running time: 0h0m40s