[2024-01-24 11:26:28,011] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:28,012] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:28,013] [INFO] DQC Reference Directory: /var/lib/cwl/stg4a89fe27-dbb7-45ba-a4cf-8149441b1196/dqc_reference
[2024-01-24 11:26:29,441] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:29,441] [INFO] Task started: Prodigal
[2024-01-24 11:26:29,442] [INFO] Running command: gunzip -c /var/lib/cwl/stga2acb3cb-c4e2-4552-969b-ce1970a5e29b/GCF_025995755.1_ASM2599575v1_genomic.fna.gz | prodigal -d GCF_025995755.1_ASM2599575v1_genomic.fna/cds.fna -a GCF_025995755.1_ASM2599575v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:38,505] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:38,506] [INFO] Task started: HMMsearch
[2024-01-24 11:26:38,506] [INFO] Running command: hmmsearch --tblout GCF_025995755.1_ASM2599575v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4a89fe27-dbb7-45ba-a4cf-8149441b1196/dqc_reference/reference_markers.hmm GCF_025995755.1_ASM2599575v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:38,776] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:38,778] [INFO] Found 6/6 markers.
[2024-01-24 11:26:38,815] [INFO] Query marker FASTA was written to GCF_025995755.1_ASM2599575v1_genomic.fna/markers.fasta
[2024-01-24 11:26:38,816] [INFO] Task started: Blastn
[2024-01-24 11:26:38,816] [INFO] Running command: blastn -query GCF_025995755.1_ASM2599575v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a89fe27-dbb7-45ba-a4cf-8149441b1196/dqc_reference/reference_markers.fasta -out GCF_025995755.1_ASM2599575v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:39,518] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:39,521] [INFO] Selected 6 target genomes.
[2024-01-24 11:26:39,521] [INFO] Target genome list was writen to GCF_025995755.1_ASM2599575v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:39,525] [INFO] Task started: fastANI
[2024-01-24 11:26:39,525] [INFO] Running command: fastANI --query /var/lib/cwl/stga2acb3cb-c4e2-4552-969b-ce1970a5e29b/GCF_025995755.1_ASM2599575v1_genomic.fna.gz --refList GCF_025995755.1_ASM2599575v1_genomic.fna/target_genomes.txt --output GCF_025995755.1_ASM2599575v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:43,612] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:43,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4a89fe27-dbb7-45ba-a4cf-8149441b1196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:43,613] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4a89fe27-dbb7-45ba-a4cf-8149441b1196/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:43,620] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:26:43,620] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:43,620] [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 ghanensis	strain=LMG 23848	GCA_011516865.1	431306	431306	type	True	99.9955	868	872	95	conclusive
Acetobacter ghanensis	strain=LMG 23848T	GCA_001499675.1	431306	431306	type	True	99.9866	871	872	95	conclusive
Acetobacter fabarum	strain=LMG 24244	GCA_011516925.1	483199	483199	type	True	85.7028	665	872	95	below_threshold
Acetobacter lovaniensis	strain=DSM 4491	GCA_014207635.1	104100	104100	type	True	85.2268	660	872	95	below_threshold
Acetobacter lovaniensis	strain=LMG 1617	GCA_011516875.1	104100	104100	type	True	85.1735	668	872	95	below_threshold
Acetobacter cerevisiae	strain=LMG 1625	GCA_001580535.1	178900	178900	type	True	79.1404	342	872	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:43,622] [INFO] DFAST Taxonomy check result was written to GCF_025995755.1_ASM2599575v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:43,623] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:43,623] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:43,623] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4a89fe27-dbb7-45ba-a4cf-8149441b1196/dqc_reference/checkm_data
[2024-01-24 11:26:43,625] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:43,656] [INFO] Task started: CheckM
[2024-01-24 11:26:43,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995755.1_ASM2599575v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995755.1_ASM2599575v1_genomic.fna/checkm_input GCF_025995755.1_ASM2599575v1_genomic.fna/checkm_result
[2024-01-24 11:27:13,740] [INFO] Task succeeded: CheckM
[2024-01-24 11:27:13,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:27:13,760] [INFO] ===== Completeness check finished =====
[2024-01-24 11:27:13,761] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:27:13,761] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995755.1_ASM2599575v1_genomic.fna/markers.fasta)
[2024-01-24 11:27:13,762] [INFO] Task started: Blastn
[2024-01-24 11:27:13,762] [INFO] Running command: blastn -query GCF_025995755.1_ASM2599575v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4a89fe27-dbb7-45ba-a4cf-8149441b1196/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995755.1_ASM2599575v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:27:14,963] [INFO] Task succeeded: Blastn
[2024-01-24 11:27:14,972] [INFO] Selected 10 target genomes.
[2024-01-24 11:27:14,972] [INFO] Target genome list was writen to GCF_025995755.1_ASM2599575v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:27:14,983] [INFO] Task started: fastANI
[2024-01-24 11:27:14,984] [INFO] Running command: fastANI --query /var/lib/cwl/stga2acb3cb-c4e2-4552-969b-ce1970a5e29b/GCF_025995755.1_ASM2599575v1_genomic.fna.gz --refList GCF_025995755.1_ASM2599575v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995755.1_ASM2599575v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:27:21,157] [INFO] Task succeeded: fastANI
[2024-01-24 11:27:21,166] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:27:21,167] [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_001499675.1	s__Acetobacter ghanensis	99.9866	871	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_011516925.1	s__Acetobacter fabarum	85.711	664	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.96	97.82	0.89	0.87	4	-
GCF_011516885.1	s__Acetobacter lambici	85.5131	667	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014207635.1	s__Acetobacter lovaniensis	85.2109	661	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000964225.1	s__Acetobacter syzygii	84.5793	630	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.87	98.22	0.97	0.90	7	-
GCF_002153655.1	s__Acetobacter okinawensis_A	84.432	638	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000613865.1	s__Acetobacter okinawensis	84.3167	647	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.60	97.58	0.84	0.82	3	-
GCF_001580535.1	s__Acetobacter cerevisiae	79.1544	341	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_011516935.1	s__Acetobacter farinalis	78.505	303	872	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:27:21,168] [INFO] GTDB search result was written to GCF_025995755.1_ASM2599575v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:27:21,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:27:21,172] [INFO] DFAST_QC result json was written to GCF_025995755.1_ASM2599575v1_genomic.fna/dqc_result.json
[2024-01-24 11:27:21,172] [INFO] DFAST_QC completed!
[2024-01-24 11:27:21,172] [INFO] Total running time: 0h0m53s