[2024-01-24 13:13:06,493] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:06,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:06,497] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c9d263c-ee26-49e4-89d2-9dacc2abddb4/dqc_reference
[2024-01-24 13:13:07,807] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:07,807] [INFO] Task started: Prodigal
[2024-01-24 13:13:07,808] [INFO] Running command: gunzip -c /var/lib/cwl/stgf61c1aa8-1e5f-476b-ba8a-e650d6ad130d/GCF_025994595.1_ASM2599459v1_genomic.fna.gz | prodigal -d GCF_025994595.1_ASM2599459v1_genomic.fna/cds.fna -a GCF_025994595.1_ASM2599459v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:20,023] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:20,024] [INFO] Task started: HMMsearch
[2024-01-24 13:13:20,024] [INFO] Running command: hmmsearch --tblout GCF_025994595.1_ASM2599459v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c9d263c-ee26-49e4-89d2-9dacc2abddb4/dqc_reference/reference_markers.hmm GCF_025994595.1_ASM2599459v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:20,294] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:20,295] [INFO] Found 6/6 markers.
[2024-01-24 13:13:20,327] [INFO] Query marker FASTA was written to GCF_025994595.1_ASM2599459v1_genomic.fna/markers.fasta
[2024-01-24 13:13:20,328] [INFO] Task started: Blastn
[2024-01-24 13:13:20,328] [INFO] Running command: blastn -query GCF_025994595.1_ASM2599459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c9d263c-ee26-49e4-89d2-9dacc2abddb4/dqc_reference/reference_markers.fasta -out GCF_025994595.1_ASM2599459v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:21,197] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:21,200] [INFO] Selected 10 target genomes.
[2024-01-24 13:13:21,200] [INFO] Target genome list was writen to GCF_025994595.1_ASM2599459v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:21,302] [INFO] Task started: fastANI
[2024-01-24 13:13:21,302] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61c1aa8-1e5f-476b-ba8a-e650d6ad130d/GCF_025994595.1_ASM2599459v1_genomic.fna.gz --refList GCF_025994595.1_ASM2599459v1_genomic.fna/target_genomes.txt --output GCF_025994595.1_ASM2599459v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:29,660] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:29,661] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c9d263c-ee26-49e4-89d2-9dacc2abddb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:29,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c9d263c-ee26-49e4-89d2-9dacc2abddb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:29,670] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:13:29,671] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:13:29,671] [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
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	99.9939	1159	1164	95	conclusive
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	91.9969	920	1164	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	91.2494	929	1164	95	below_threshold
Komagataeibacter intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	89.52	821	1164	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	89.2741	845	1164	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.9246	348	1164	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	78.3437	200	1164	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.4502	149	1164	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.6151	173	1164	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.5632	97	1164	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:29,673] [INFO] DFAST Taxonomy check result was written to GCF_025994595.1_ASM2599459v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:29,673] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:29,674] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:29,674] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c9d263c-ee26-49e4-89d2-9dacc2abddb4/dqc_reference/checkm_data
[2024-01-24 13:13:29,675] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:29,717] [INFO] Task started: CheckM
[2024-01-24 13:13:29,718] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994595.1_ASM2599459v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994595.1_ASM2599459v1_genomic.fna/checkm_input GCF_025994595.1_ASM2599459v1_genomic.fna/checkm_result
[2024-01-24 13:14:09,514] [INFO] Task succeeded: CheckM
[2024-01-24 13:14:09,515] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:14:09,530] [INFO] ===== Completeness check finished =====
[2024-01-24 13:14:09,531] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:14:09,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994595.1_ASM2599459v1_genomic.fna/markers.fasta)
[2024-01-24 13:14:09,532] [INFO] Task started: Blastn
[2024-01-24 13:14:09,532] [INFO] Running command: blastn -query GCF_025994595.1_ASM2599459v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c9d263c-ee26-49e4-89d2-9dacc2abddb4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994595.1_ASM2599459v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:14:10,990] [INFO] Task succeeded: Blastn
[2024-01-24 13:14:10,993] [INFO] Selected 6 target genomes.
[2024-01-24 13:14:10,994] [INFO] Target genome list was writen to GCF_025994595.1_ASM2599459v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:14:11,021] [INFO] Task started: fastANI
[2024-01-24 13:14:11,022] [INFO] Running command: fastANI --query /var/lib/cwl/stgf61c1aa8-1e5f-476b-ba8a-e650d6ad130d/GCF_025994595.1_ASM2599459v1_genomic.fna.gz --refList GCF_025994595.1_ASM2599459v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994595.1_ASM2599459v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:14:17,115] [INFO] Task succeeded: fastANI
[2024-01-24 13:14:17,130] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:14:17,131] [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_003207895.1	s__Komagataeibacter swingsii	99.9939	1159	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	conclusive
GCF_000285295.1	s__Komagataeibacter europaeus	91.9969	920	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_015155755.1	s__Komagataeibacter sp015155755	91.6169	875	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006538165.1	s__Komagataeibacter diospyri	91.2494	929	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
GCF_000964425.1	s__Komagataeibacter intermedius	89.5383	820	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_003207815.1	s__Komagataeibacter oboediens	89.2604	845	1164	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.65	98.22	0.88	0.85	10	-
--------------------------------------------------------------------------------
[2024-01-24 13:14:17,133] [INFO] GTDB search result was written to GCF_025994595.1_ASM2599459v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:14:17,134] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:14:17,138] [INFO] DFAST_QC result json was written to GCF_025994595.1_ASM2599459v1_genomic.fna/dqc_result.json
[2024-01-24 13:14:17,139] [INFO] DFAST_QC completed!
[2024-01-24 13:14:17,139] [INFO] Total running time: 0h1m11s