[2024-01-24 12:29:28,659] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:29:28,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:29:28,661] [INFO] DQC Reference Directory: /var/lib/cwl/stg0245851c-7ca4-4d5c-934a-0b53b8382449/dqc_reference
[2024-01-24 12:29:30,176] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:29:30,177] [INFO] Task started: Prodigal
[2024-01-24 12:29:30,177] [INFO] Running command: gunzip -c /var/lib/cwl/stg99c97a42-ff37-47de-891b-e750bd2a49f7/GCF_001571345.1_ASM157134v1_genomic.fna.gz | prodigal -d GCF_001571345.1_ASM157134v1_genomic.fna/cds.fna -a GCF_001571345.1_ASM157134v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:29:42,163] [INFO] Task succeeded: Prodigal
[2024-01-24 12:29:42,164] [INFO] Task started: HMMsearch
[2024-01-24 12:29:42,164] [INFO] Running command: hmmsearch --tblout GCF_001571345.1_ASM157134v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0245851c-7ca4-4d5c-934a-0b53b8382449/dqc_reference/reference_markers.hmm GCF_001571345.1_ASM157134v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:29:42,517] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:29:42,518] [INFO] Found 6/6 markers.
[2024-01-24 12:29:42,568] [INFO] Query marker FASTA was written to GCF_001571345.1_ASM157134v1_genomic.fna/markers.fasta
[2024-01-24 12:29:42,568] [INFO] Task started: Blastn
[2024-01-24 12:29:42,569] [INFO] Running command: blastn -query GCF_001571345.1_ASM157134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0245851c-7ca4-4d5c-934a-0b53b8382449/dqc_reference/reference_markers.fasta -out GCF_001571345.1_ASM157134v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:43,373] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:43,377] [INFO] Selected 10 target genomes.
[2024-01-24 12:29:43,378] [INFO] Target genome list was writen to GCF_001571345.1_ASM157134v1_genomic.fna/target_genomes.txt
[2024-01-24 12:29:43,382] [INFO] Task started: fastANI
[2024-01-24 12:29:43,382] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c97a42-ff37-47de-891b-e750bd2a49f7/GCF_001571345.1_ASM157134v1_genomic.fna.gz --refList GCF_001571345.1_ASM157134v1_genomic.fna/target_genomes.txt --output GCF_001571345.1_ASM157134v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:29:52,148] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:52,149] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0245851c-7ca4-4d5c-934a-0b53b8382449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:29:52,149] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0245851c-7ca4-4d5c-934a-0b53b8382449/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:29:52,160] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:29:52,160] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:29:52,160] [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=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	100.0	1132	1138	95	conclusive
Komagataeibacter xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	99.9697	1114	1138	95	conclusive
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	92.7876	904	1138	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	92.6543	909	1138	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	92.4348	909	1138	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.9179	335	1138	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.4363	161	1138	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.4722	111	1138	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.4448	176	1138	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.9492	65	1138	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:29:52,162] [INFO] DFAST Taxonomy check result was written to GCF_001571345.1_ASM157134v1_genomic.fna/tc_result.tsv
[2024-01-24 12:29:52,163] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:29:52,163] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:29:52,163] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0245851c-7ca4-4d5c-934a-0b53b8382449/dqc_reference/checkm_data
[2024-01-24 12:29:52,164] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:29:52,201] [INFO] Task started: CheckM
[2024-01-24 12:29:52,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001571345.1_ASM157134v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001571345.1_ASM157134v1_genomic.fna/checkm_input GCF_001571345.1_ASM157134v1_genomic.fna/checkm_result
[2024-01-24 12:30:32,533] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:32,534] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:32,558] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:32,559] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:32,559] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001571345.1_ASM157134v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:32,560] [INFO] Task started: Blastn
[2024-01-24 12:30:32,560] [INFO] Running command: blastn -query GCF_001571345.1_ASM157134v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0245851c-7ca4-4d5c-934a-0b53b8382449/dqc_reference/reference_markers_gtdb.fasta -out GCF_001571345.1_ASM157134v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:33,803] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:33,808] [INFO] Selected 8 target genomes.
[2024-01-24 12:30:33,808] [INFO] Target genome list was writen to GCF_001571345.1_ASM157134v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:33,817] [INFO] Task started: fastANI
[2024-01-24 12:30:33,817] [INFO] Running command: fastANI --query /var/lib/cwl/stg99c97a42-ff37-47de-891b-e750bd2a49f7/GCF_001571345.1_ASM157134v1_genomic.fna.gz --refList GCF_001571345.1_ASM157134v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001571345.1_ASM157134v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:41,816] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:41,824] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:41,824] [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	100.0	1132	1138	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	94.0487	938	1138	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	92.8209	947	1138	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	92.8149	901	1138	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.98	99.98	0.98	0.98	2	-
GCF_003207865.1	s__Komagataeibacter sucrofermentans	92.6543	909	1138	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	92.4348	909	1138	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	78.4138	199	1138	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	77.9	183	1138	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 12:30:41,826] [INFO] GTDB search result was written to GCF_001571345.1_ASM157134v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:41,827] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:41,840] [INFO] DFAST_QC result json was written to GCF_001571345.1_ASM157134v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:41,841] [INFO] DFAST_QC completed!
[2024-01-24 12:30:41,841] [INFO] Total running time: 0h1m13s