[2024-01-24 11:43:53,206] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:43:53,209] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:43:53,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg77639e63-ed61-4faa-afe1-e647c3172f3e/dqc_reference
[2024-01-24 11:43:54,462] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:43:54,463] [INFO] Task started: Prodigal
[2024-01-24 11:43:54,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg0396a3f6-7760-45ac-9a2e-1aef6cf3fe22/GCF_003403295.1_ASM340329v1_genomic.fna.gz | prodigal -d GCF_003403295.1_ASM340329v1_genomic.fna/cds.fna -a GCF_003403295.1_ASM340329v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:05,125] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:05,126] [INFO] Task started: HMMsearch
[2024-01-24 11:44:05,126] [INFO] Running command: hmmsearch --tblout GCF_003403295.1_ASM340329v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77639e63-ed61-4faa-afe1-e647c3172f3e/dqc_reference/reference_markers.hmm GCF_003403295.1_ASM340329v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:05,324] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:05,325] [INFO] Found 6/6 markers.
[2024-01-24 11:44:05,355] [INFO] Query marker FASTA was written to GCF_003403295.1_ASM340329v1_genomic.fna/markers.fasta
[2024-01-24 11:44:05,355] [INFO] Task started: Blastn
[2024-01-24 11:44:05,355] [INFO] Running command: blastn -query GCF_003403295.1_ASM340329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77639e63-ed61-4faa-afe1-e647c3172f3e/dqc_reference/reference_markers.fasta -out GCF_003403295.1_ASM340329v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:06,195] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:06,198] [INFO] Selected 18 target genomes.
[2024-01-24 11:44:06,199] [INFO] Target genome list was writen to GCF_003403295.1_ASM340329v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:06,205] [INFO] Task started: fastANI
[2024-01-24 11:44:06,205] [INFO] Running command: fastANI --query /var/lib/cwl/stg0396a3f6-7760-45ac-9a2e-1aef6cf3fe22/GCF_003403295.1_ASM340329v1_genomic.fna.gz --refList GCF_003403295.1_ASM340329v1_genomic.fna/target_genomes.txt --output GCF_003403295.1_ASM340329v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:18,827] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:18,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77639e63-ed61-4faa-afe1-e647c3172f3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:18,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77639e63-ed61-4faa-afe1-e647c3172f3e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:18,842] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:18,843] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:18,843] [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 melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	100.0	1061	1070	95	conclusive
Komagataeibacter kakiaceti	strain=JCM 25156	GCA_000613305.1	943261	943261	type	True	88.6736	448	1070	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	85.9821	753	1070	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	85.4424	727	1070	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	85.4297	709	1070	95	below_threshold
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	85.4257	754	1070	95	below_threshold
Komagataeibacter intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	85.1453	725	1070	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	85.1409	736	1070	95	below_threshold
Komagataeibacter xylinus	strain=LMG 1515	GCA_003207915.1	28448	28448	suspected-type	True	85.1	739	1070	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	85.0586	726	1070	95	below_threshold
Komagataeibacter saccharivorans	strain=LMG 1582	GCA_003207825.1	265959	265959	type	True	85.057	735	1070	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	84.7926	734	1070	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	84.5916	733	1070	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.7648	331	1070	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	77.945	214	1070	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.67	134	1070	95	below_threshold
Roseomonas rubea	strain=MO17	GCA_016106015.1	2748666	2748666	type	True	76.6074	114	1070	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.3478	101	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:18,844] [INFO] DFAST Taxonomy check result was written to GCF_003403295.1_ASM340329v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:18,845] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:18,845] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:18,845] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77639e63-ed61-4faa-afe1-e647c3172f3e/dqc_reference/checkm_data
[2024-01-24 11:44:18,847] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:18,884] [INFO] Task started: CheckM
[2024-01-24 11:44:18,884] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003403295.1_ASM340329v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003403295.1_ASM340329v1_genomic.fna/checkm_input GCF_003403295.1_ASM340329v1_genomic.fna/checkm_result
[2024-01-24 11:44:53,152] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:53,153] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:53,171] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:53,171] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:53,171] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003403295.1_ASM340329v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:53,172] [INFO] Task started: Blastn
[2024-01-24 11:44:53,172] [INFO] Running command: blastn -query GCF_003403295.1_ASM340329v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77639e63-ed61-4faa-afe1-e647c3172f3e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003403295.1_ASM340329v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:54,605] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:54,608] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:54,608] [INFO] Target genome list was writen to GCF_003403295.1_ASM340329v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:54,616] [INFO] Task started: fastANI
[2024-01-24 11:44:54,616] [INFO] Running command: fastANI --query /var/lib/cwl/stg0396a3f6-7760-45ac-9a2e-1aef6cf3fe22/GCF_003403295.1_ASM340329v1_genomic.fna.gz --refList GCF_003403295.1_ASM340329v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003403295.1_ASM340329v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:45:05,038] [INFO] Task succeeded: fastANI
[2024-01-24 11:45:05,049] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:45:05,049] [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_003403295.1	s__Komagataeibacter melaceti	100.0	1061	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014199155.1	s__Komagataeibacter kakiaceti	89.6623	874	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_003207895.1	s__Komagataeibacter swingsii	85.9749	754	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_015155755.1	s__Komagataeibacter sp015155755	85.5227	701	1070	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	85.4964	747	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000285295.1	s__Komagataeibacter europaeus	85.4593	751	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_013155395.1	s__Komagataeibacter melomenusus	85.459	724	1070	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	85.4389	709	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000964425.1	s__Komagataeibacter intermedius	85.1571	724	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_003207825.1	s__Komagataeibacter saccharivorans	85.089	733	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.47	98.42	0.92	0.87	4	-
GCF_003207795.1	s__Komagataeibacter nataicola	85.062	726	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.90	99.90	0.97	0.97	2	-
GCF_003207815.1	s__Komagataeibacter oboediens	84.7861	735	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.65	98.22	0.88	0.85	10	-
GCF_006538165.1	s__Komagataeibacter diospyri	84.5975	732	1070	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:45:05,051] [INFO] GTDB search result was written to GCF_003403295.1_ASM340329v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:45:05,051] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:45:05,055] [INFO] DFAST_QC result json was written to GCF_003403295.1_ASM340329v1_genomic.fna/dqc_result.json
[2024-01-24 11:45:05,055] [INFO] DFAST_QC completed!
[2024-01-24 11:45:05,055] [INFO] Total running time: 0h1m12s