[2024-01-24 13:58:41,420] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:58:41,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:58:41,423] [INFO] DQC Reference Directory: /var/lib/cwl/stg031dccdf-296e-4707-a01d-52cf04a2da8f/dqc_reference
[2024-01-24 13:58:42,737] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:58:42,738] [INFO] Task started: Prodigal
[2024-01-24 13:58:42,739] [INFO] Running command: gunzip -c /var/lib/cwl/stg14a50228-ee15-4306-b0c6-97002e818230/GCF_025994615.1_ASM2599461v1_genomic.fna.gz | prodigal -d GCF_025994615.1_ASM2599461v1_genomic.fna/cds.fna -a GCF_025994615.1_ASM2599461v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:58:55,480] [INFO] Task succeeded: Prodigal
[2024-01-24 13:58:55,481] [INFO] Task started: HMMsearch
[2024-01-24 13:58:55,481] [INFO] Running command: hmmsearch --tblout GCF_025994615.1_ASM2599461v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg031dccdf-296e-4707-a01d-52cf04a2da8f/dqc_reference/reference_markers.hmm GCF_025994615.1_ASM2599461v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:58:55,816] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:58:55,818] [INFO] Found 6/6 markers.
[2024-01-24 13:58:55,860] [INFO] Query marker FASTA was written to GCF_025994615.1_ASM2599461v1_genomic.fna/markers.fasta
[2024-01-24 13:58:55,861] [INFO] Task started: Blastn
[2024-01-24 13:58:55,861] [INFO] Running command: blastn -query GCF_025994615.1_ASM2599461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg031dccdf-296e-4707-a01d-52cf04a2da8f/dqc_reference/reference_markers.fasta -out GCF_025994615.1_ASM2599461v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:56,734] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:56,737] [INFO] Selected 10 target genomes.
[2024-01-24 13:58:56,738] [INFO] Target genome list was writen to GCF_025994615.1_ASM2599461v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:56,747] [INFO] Task started: fastANI
[2024-01-24 13:58:56,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg14a50228-ee15-4306-b0c6-97002e818230/GCF_025994615.1_ASM2599461v1_genomic.fna.gz --refList GCF_025994615.1_ASM2599461v1_genomic.fna/target_genomes.txt --output GCF_025994615.1_ASM2599461v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:59:05,044] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,044] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg031dccdf-296e-4707-a01d-52cf04a2da8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:59:05,045] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg031dccdf-296e-4707-a01d-52cf04a2da8f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:59:05,056] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:59:05,056] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:59:05,056] [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 xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	99.9951	1076	1079	95	conclusive
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	99.9798	1049	1079	95	conclusive
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	92.9312	864	1079	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	92.7304	875	1079	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	92.5393	879	1079	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.9948	319	1079	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.3423	156	1079	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.7169	109	1079	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.5251	172	1079	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	76.1859	55	1079	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,058] [INFO] DFAST Taxonomy check result was written to GCF_025994615.1_ASM2599461v1_genomic.fna/tc_result.tsv
[2024-01-24 13:59:05,059] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:59:05,059] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:59:05,059] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg031dccdf-296e-4707-a01d-52cf04a2da8f/dqc_reference/checkm_data
[2024-01-24 13:59:05,061] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:59:05,098] [INFO] Task started: CheckM
[2024-01-24 13:59:05,099] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994615.1_ASM2599461v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994615.1_ASM2599461v1_genomic.fna/checkm_input GCF_025994615.1_ASM2599461v1_genomic.fna/checkm_result
[2024-01-24 13:59:44,083] [INFO] Task succeeded: CheckM
[2024-01-24 13:59:44,085] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:59:44,104] [INFO] ===== Completeness check finished =====
[2024-01-24 13:59:44,104] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:59:44,104] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994615.1_ASM2599461v1_genomic.fna/markers.fasta)
[2024-01-24 13:59:44,105] [INFO] Task started: Blastn
[2024-01-24 13:59:44,105] [INFO] Running command: blastn -query GCF_025994615.1_ASM2599461v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg031dccdf-296e-4707-a01d-52cf04a2da8f/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994615.1_ASM2599461v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:59:45,244] [INFO] Task succeeded: Blastn
[2024-01-24 13:59:45,249] [INFO] Selected 8 target genomes.
[2024-01-24 13:59:45,249] [INFO] Target genome list was writen to GCF_025994615.1_ASM2599461v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:59:45,262] [INFO] Task started: fastANI
[2024-01-24 13:59:45,262] [INFO] Running command: fastANI --query /var/lib/cwl/stg14a50228-ee15-4306-b0c6-97002e818230/GCF_025994615.1_ASM2599461v1_genomic.fna.gz --refList GCF_025994615.1_ASM2599461v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994615.1_ASM2599461v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:52,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:52,165] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:52,165] [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_001571345.1	s__Komagataeibacter xylinus	99.9798	1049	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.56	99.15	0.93	0.88	3	conclusive
GCF_004302915.1	s__Komagataeibacter xylinus_C	93.9766	913	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013155395.1	s__Komagataeibacter melomenusus	92.9098	865	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_009834365.1	s__Komagataeibacter xylinus_D	92.8736	921	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003207865.1	s__Komagataeibacter sucrofermentans	92.7304	875	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003207795.1	s__Komagataeibacter nataicola	92.5393	879	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.90	99.90	0.97	0.97	2	-
GCA_002409645.1	s__Acetobacter sp002409645	78.2533	193	1079	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017377715.1	s__Acetobacter sacchari	77.8748	173	1079	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 13:59:52,167] [INFO] GTDB search result was written to GCF_025994615.1_ASM2599461v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:52,168] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:52,171] [INFO] DFAST_QC result json was written to GCF_025994615.1_ASM2599461v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:52,171] [INFO] DFAST_QC completed!
[2024-01-24 13:59:52,171] [INFO] Total running time: 0h1m11s