[2024-01-24 13:32:17,588] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:32:17,592] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:32:17,592] [INFO] DQC Reference Directory: /var/lib/cwl/stg076110a9-4058-4334-865e-d805c35d7fe8/dqc_reference
[2024-01-24 13:32:18,998] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:32:18,999] [INFO] Task started: Prodigal
[2024-01-24 13:32:18,999] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d33c252-5c17-4b46-9fab-0a34e61d0d87/GCF_004341445.1_ASM434144v1_genomic.fna.gz | prodigal -d GCF_004341445.1_ASM434144v1_genomic.fna/cds.fna -a GCF_004341445.1_ASM434144v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:32:25,551] [INFO] Task succeeded: Prodigal
[2024-01-24 13:32:25,552] [INFO] Task started: HMMsearch
[2024-01-24 13:32:25,552] [INFO] Running command: hmmsearch --tblout GCF_004341445.1_ASM434144v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg076110a9-4058-4334-865e-d805c35d7fe8/dqc_reference/reference_markers.hmm GCF_004341445.1_ASM434144v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:32:25,823] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:32:25,824] [INFO] Found 6/6 markers.
[2024-01-24 13:32:25,851] [INFO] Query marker FASTA was written to GCF_004341445.1_ASM434144v1_genomic.fna/markers.fasta
[2024-01-24 13:32:25,851] [INFO] Task started: Blastn
[2024-01-24 13:32:25,851] [INFO] Running command: blastn -query GCF_004341445.1_ASM434144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg076110a9-4058-4334-865e-d805c35d7fe8/dqc_reference/reference_markers.fasta -out GCF_004341445.1_ASM434144v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:32:26,464] [INFO] Task succeeded: Blastn
[2024-01-24 13:32:26,468] [INFO] Selected 21 target genomes.
[2024-01-24 13:32:26,469] [INFO] Target genome list was writen to GCF_004341445.1_ASM434144v1_genomic.fna/target_genomes.txt
[2024-01-24 13:32:26,483] [INFO] Task started: fastANI
[2024-01-24 13:32:26,483] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d33c252-5c17-4b46-9fab-0a34e61d0d87/GCF_004341445.1_ASM434144v1_genomic.fna.gz --refList GCF_004341445.1_ASM434144v1_genomic.fna/target_genomes.txt --output GCF_004341445.1_ASM434144v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:32:41,066] [INFO] Task succeeded: fastANI
[2024-01-24 13:32:41,067] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg076110a9-4058-4334-865e-d805c35d7fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:32:41,067] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg076110a9-4058-4334-865e-d805c35d7fe8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:32:41,072] [INFO] Found 2 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:32:41,072] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:32:41,072] [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
Baia soyae	strain=DSM 46831	GCA_004341445.1	1544746	1544746	type	True	100.0	927	929	95	conclusive
Risungbinella massiliensis	strain=GD1	GCA_000942395.1	1329796	1329796	type	True	76.8191	50	929	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:32:41,082] [INFO] DFAST Taxonomy check result was written to GCF_004341445.1_ASM434144v1_genomic.fna/tc_result.tsv
[2024-01-24 13:32:41,082] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:32:41,083] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:32:41,083] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg076110a9-4058-4334-865e-d805c35d7fe8/dqc_reference/checkm_data
[2024-01-24 13:32:41,084] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:32:41,126] [INFO] Task started: CheckM
[2024-01-24 13:32:41,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004341445.1_ASM434144v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004341445.1_ASM434144v1_genomic.fna/checkm_input GCF_004341445.1_ASM434144v1_genomic.fna/checkm_result
[2024-01-24 13:33:07,782] [INFO] Task succeeded: CheckM
[2024-01-24 13:33:07,783] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:33:07,824] [INFO] ===== Completeness check finished =====
[2024-01-24 13:33:07,824] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:33:07,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004341445.1_ASM434144v1_genomic.fna/markers.fasta)
[2024-01-24 13:33:07,824] [INFO] Task started: Blastn
[2024-01-24 13:33:07,825] [INFO] Running command: blastn -query GCF_004341445.1_ASM434144v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg076110a9-4058-4334-865e-d805c35d7fe8/dqc_reference/reference_markers_gtdb.fasta -out GCF_004341445.1_ASM434144v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:33:08,686] [INFO] Task succeeded: Blastn
[2024-01-24 13:33:08,689] [INFO] Selected 15 target genomes.
[2024-01-24 13:33:08,689] [INFO] Target genome list was writen to GCF_004341445.1_ASM434144v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:33:08,701] [INFO] Task started: fastANI
[2024-01-24 13:33:08,702] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d33c252-5c17-4b46-9fab-0a34e61d0d87/GCF_004341445.1_ASM434144v1_genomic.fna.gz --refList GCF_004341445.1_ASM434144v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004341445.1_ASM434144v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:33:20,964] [INFO] Task succeeded: fastANI
[2024-01-24 13:33:20,973] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:33:20,974] [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_004341445.1	s__Baia soyae	100.0	927	929	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Baia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900119485.1	s__Baia sp900119485	87.9717	779	929	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Baia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900107305.1	s__Baia sp900107305	87.5112	758	929	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Baia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000942395.1	s__Risungbinella massiliensis	76.8528	51	929	d__Bacteria;p__Firmicutes;c__Bacilli;o__Thermoactinomycetales;f__Thermoactinomycetaceae;g__Risungbinella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:33:20,975] [INFO] GTDB search result was written to GCF_004341445.1_ASM434144v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:33:20,976] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:33:20,979] [INFO] DFAST_QC result json was written to GCF_004341445.1_ASM434144v1_genomic.fna/dqc_result.json
[2024-01-24 13:33:20,979] [INFO] DFAST_QC completed!
[2024-01-24 13:33:20,980] [INFO] Total running time: 0h1m3s