[2024-01-24 14:28:15,889] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,894] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,894] [INFO] DQC Reference Directory: /var/lib/cwl/stg764ddaa7-7310-4e46-951a-3c0daeb96dd5/dqc_reference
[2024-01-24 14:28:17,937] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,938] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,939] [INFO] Running command: gunzip -c /var/lib/cwl/stg88f974b9-817b-4d9d-883d-2ba24d63cb84/GCF_000613865.1_ASM61386v1_genomic.fna.gz | prodigal -d GCF_000613865.1_ASM61386v1_genomic.fna/cds.fna -a GCF_000613865.1_ASM61386v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:28,072] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:28,072] [INFO] Task started: HMMsearch
[2024-01-24 14:28:28,072] [INFO] Running command: hmmsearch --tblout GCF_000613865.1_ASM61386v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg764ddaa7-7310-4e46-951a-3c0daeb96dd5/dqc_reference/reference_markers.hmm GCF_000613865.1_ASM61386v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:28,322] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:28,323] [INFO] Found 6/6 markers.
[2024-01-24 14:28:28,362] [INFO] Query marker FASTA was written to GCF_000613865.1_ASM61386v1_genomic.fna/markers.fasta
[2024-01-24 14:28:28,362] [INFO] Task started: Blastn
[2024-01-24 14:28:28,362] [INFO] Running command: blastn -query GCF_000613865.1_ASM61386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg764ddaa7-7310-4e46-951a-3c0daeb96dd5/dqc_reference/reference_markers.fasta -out GCF_000613865.1_ASM61386v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:29,070] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:29,074] [INFO] Selected 12 target genomes.
[2024-01-24 14:28:29,074] [INFO] Target genome list was writen to GCF_000613865.1_ASM61386v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:29,142] [INFO] Task started: fastANI
[2024-01-24 14:28:29,142] [INFO] Running command: fastANI --query /var/lib/cwl/stg88f974b9-817b-4d9d-883d-2ba24d63cb84/GCF_000613865.1_ASM61386v1_genomic.fna.gz --refList GCF_000613865.1_ASM61386v1_genomic.fna/target_genomes.txt --output GCF_000613865.1_ASM61386v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:38,234] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:38,235] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg764ddaa7-7310-4e46-951a-3c0daeb96dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:38,235] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg764ddaa7-7310-4e46-951a-3c0daeb96dd5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:38,243] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:38,244] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:38,244] [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
Acetobacter okinawensis	strain=JCM 25146	GCA_000613865.1	1076594	1076594	type	True	100.0	996	999	95	conclusive
Acetobacter lambici	strain=LMG 27439	GCA_011516885.1	1332824	1332824	type	True	85.9227	661	999	95	below_threshold
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	85.7743	709	999	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	85.6876	700	999	95	below_threshold
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	85.6644	701	999	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	84.457	660	999	95	below_threshold
Acetobacter ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	84.4179	653	999	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.4885	380	999	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:38,245] [INFO] DFAST Taxonomy check result was written to GCF_000613865.1_ASM61386v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:38,246] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:38,246] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:38,246] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg764ddaa7-7310-4e46-951a-3c0daeb96dd5/dqc_reference/checkm_data
[2024-01-24 14:28:38,248] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:38,283] [INFO] Task started: CheckM
[2024-01-24 14:28:38,283] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000613865.1_ASM61386v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000613865.1_ASM61386v1_genomic.fna/checkm_input GCF_000613865.1_ASM61386v1_genomic.fna/checkm_result
[2024-01-24 14:29:10,503] [INFO] Task succeeded: CheckM
[2024-01-24 14:29:10,505] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.20%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:29:10,528] [INFO] ===== Completeness check finished =====
[2024-01-24 14:29:10,528] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:29:10,529] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000613865.1_ASM61386v1_genomic.fna/markers.fasta)
[2024-01-24 14:29:10,529] [INFO] Task started: Blastn
[2024-01-24 14:29:10,529] [INFO] Running command: blastn -query GCF_000613865.1_ASM61386v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg764ddaa7-7310-4e46-951a-3c0daeb96dd5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000613865.1_ASM61386v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:29:11,577] [INFO] Task succeeded: Blastn
[2024-01-24 14:29:11,581] [INFO] Selected 6 target genomes.
[2024-01-24 14:29:11,581] [INFO] Target genome list was writen to GCF_000613865.1_ASM61386v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:29:11,591] [INFO] Task started: fastANI
[2024-01-24 14:29:11,591] [INFO] Running command: fastANI --query /var/lib/cwl/stg88f974b9-817b-4d9d-883d-2ba24d63cb84/GCF_000613865.1_ASM61386v1_genomic.fna.gz --refList GCF_000613865.1_ASM61386v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000613865.1_ASM61386v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:29:16,013] [INFO] Task succeeded: fastANI
[2024-01-24 14:29:16,019] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:29:16,019] [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_000613865.1	s__Acetobacter okinawensis	100.0	996	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	conclusive
GCF_002153655.1	s__Acetobacter okinawensis_A	94.835	751	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516885.1	s__Acetobacter lambici	85.9059	662	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516925.1	s__Acetobacter fabarum	85.7795	709	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_014207635.1	s__Acetobacter lovaniensis	85.6863	700	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001499675.1	s__Acetobacter ghanensis	84.4573	660	999	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:29:16,021] [INFO] GTDB search result was written to GCF_000613865.1_ASM61386v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:29:16,022] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:29:16,024] [INFO] DFAST_QC result json was written to GCF_000613865.1_ASM61386v1_genomic.fna/dqc_result.json
[2024-01-24 14:29:16,024] [INFO] DFAST_QC completed!
[2024-01-24 14:29:16,024] [INFO] Total running time: 0h1m0s