[2024-01-24 14:46:55,642] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,645] [INFO] DQC Reference Directory: /var/lib/cwl/stgfcf1042f-f35e-4d87-a35c-5dcca0cbad79/dqc_reference
[2024-01-24 14:46:58,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,017] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,018] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e08e023-6f0f-4119-bb70-83a9e8641611/GCF_003207795.1_ASM320779v1_genomic.fna.gz | prodigal -d GCF_003207795.1_ASM320779v1_genomic.fna/cds.fna -a GCF_003207795.1_ASM320779v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:10,376] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:10,376] [INFO] Task started: HMMsearch
[2024-01-24 14:47:10,376] [INFO] Running command: hmmsearch --tblout GCF_003207795.1_ASM320779v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfcf1042f-f35e-4d87-a35c-5dcca0cbad79/dqc_reference/reference_markers.hmm GCF_003207795.1_ASM320779v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:10,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:10,651] [INFO] Found 6/6 markers.
[2024-01-24 14:47:10,684] [INFO] Query marker FASTA was written to GCF_003207795.1_ASM320779v1_genomic.fna/markers.fasta
[2024-01-24 14:47:10,685] [INFO] Task started: Blastn
[2024-01-24 14:47:10,685] [INFO] Running command: blastn -query GCF_003207795.1_ASM320779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf1042f-f35e-4d87-a35c-5dcca0cbad79/dqc_reference/reference_markers.fasta -out GCF_003207795.1_ASM320779v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:11,657] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:11,661] [INFO] Selected 10 target genomes.
[2024-01-24 14:47:11,662] [INFO] Target genome list was writen to GCF_003207795.1_ASM320779v1_genomic.fna/target_genomes.txt
[2024-01-24 14:47:11,678] [INFO] Task started: fastANI
[2024-01-24 14:47:11,679] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e08e023-6f0f-4119-bb70-83a9e8641611/GCF_003207795.1_ASM320779v1_genomic.fna.gz --refList GCF_003207795.1_ASM320779v1_genomic.fna/target_genomes.txt --output GCF_003207795.1_ASM320779v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:20,127] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:20,128] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfcf1042f-f35e-4d87-a35c-5dcca0cbad79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:20,128] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfcf1042f-f35e-4d87-a35c-5dcca0cbad79/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:20,137] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:20,137] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:20,137] [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 nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	100.0	1162	1170	95	conclusive
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	93.1215	947	1170	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	92.4336	915	1170	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	92.4172	886	1170	95	below_threshold
Komagataeibacter xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	92.3221	927	1170	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.4943	353	1170	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.4304	163	1170	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.5719	105	1170	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.3782	165	1170	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.9151	110	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:20,139] [INFO] DFAST Taxonomy check result was written to GCF_003207795.1_ASM320779v1_genomic.fna/tc_result.tsv
[2024-01-24 14:47:20,140] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:20,140] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:20,140] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfcf1042f-f35e-4d87-a35c-5dcca0cbad79/dqc_reference/checkm_data
[2024-01-24 14:47:20,142] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:20,182] [INFO] Task started: CheckM
[2024-01-24 14:47:20,182] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003207795.1_ASM320779v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003207795.1_ASM320779v1_genomic.fna/checkm_input GCF_003207795.1_ASM320779v1_genomic.fna/checkm_result
[2024-01-24 14:48:00,255] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:00,257] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:00,289] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:00,289] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:00,290] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003207795.1_ASM320779v1_genomic.fna/markers.fasta)
[2024-01-24 14:48:00,290] [INFO] Task started: Blastn
[2024-01-24 14:48:00,290] [INFO] Running command: blastn -query GCF_003207795.1_ASM320779v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgfcf1042f-f35e-4d87-a35c-5dcca0cbad79/dqc_reference/reference_markers_gtdb.fasta -out GCF_003207795.1_ASM320779v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:01,865] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:01,869] [INFO] Selected 6 target genomes.
[2024-01-24 14:48:01,869] [INFO] Target genome list was writen to GCF_003207795.1_ASM320779v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:01,875] [INFO] Task started: fastANI
[2024-01-24 14:48:01,875] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e08e023-6f0f-4119-bb70-83a9e8641611/GCF_003207795.1_ASM320779v1_genomic.fna.gz --refList GCF_003207795.1_ASM320779v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003207795.1_ASM320779v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:08,116] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:08,129] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:08,130] [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_003207795.1	s__Komagataeibacter nataicola	100.0	1162	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.90	99.90	0.97	0.97	2	conclusive
GCF_003207865.1	s__Komagataeibacter sucrofermentans	93.1511	945	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	92.5695	971	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834365.1	s__Komagataeibacter xylinus_D	92.4116	973	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001571345.1	s__Komagataeibacter xylinus	92.4042	916	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.56	99.15	0.93	0.88	3	-
GCF_013155395.1	s__Komagataeibacter melomenusus	92.392	887	1170	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.98	99.98	0.98	0.98	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:08,131] [INFO] GTDB search result was written to GCF_003207795.1_ASM320779v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:08,132] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:08,134] [INFO] DFAST_QC result json was written to GCF_003207795.1_ASM320779v1_genomic.fna/dqc_result.json
[2024-01-24 14:48:08,135] [INFO] DFAST_QC completed!
[2024-01-24 14:48:08,135] [INFO] Total running time: 0h1m12s