[2024-01-24 11:51:06,259] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:06,261] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:06,261] [INFO] DQC Reference Directory: /var/lib/cwl/stg72316e02-173b-46f5-a8bf-b1814f13da70/dqc_reference
[2024-01-24 11:51:07,539] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:07,540] [INFO] Task started: Prodigal
[2024-01-24 11:51:07,540] [INFO] Running command: gunzip -c /var/lib/cwl/stg5be220ac-c0f4-44b2-8578-fd57b64fc215/GCF_025994515.1_ASM2599451v1_genomic.fna.gz | prodigal -d GCF_025994515.1_ASM2599451v1_genomic.fna/cds.fna -a GCF_025994515.1_ASM2599451v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:18,796] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:18,797] [INFO] Task started: HMMsearch
[2024-01-24 11:51:18,797] [INFO] Running command: hmmsearch --tblout GCF_025994515.1_ASM2599451v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg72316e02-173b-46f5-a8bf-b1814f13da70/dqc_reference/reference_markers.hmm GCF_025994515.1_ASM2599451v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:19,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:19,087] [INFO] Found 6/6 markers.
[2024-01-24 11:51:19,123] [INFO] Query marker FASTA was written to GCF_025994515.1_ASM2599451v1_genomic.fna/markers.fasta
[2024-01-24 11:51:19,123] [INFO] Task started: Blastn
[2024-01-24 11:51:19,123] [INFO] Running command: blastn -query GCF_025994515.1_ASM2599451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72316e02-173b-46f5-a8bf-b1814f13da70/dqc_reference/reference_markers.fasta -out GCF_025994515.1_ASM2599451v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:19,974] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:19,978] [INFO] Selected 17 target genomes.
[2024-01-24 11:51:19,979] [INFO] Target genome list was writen to GCF_025994515.1_ASM2599451v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:20,003] [INFO] Task started: fastANI
[2024-01-24 11:51:20,003] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be220ac-c0f4-44b2-8578-fd57b64fc215/GCF_025994515.1_ASM2599451v1_genomic.fna.gz --refList GCF_025994515.1_ASM2599451v1_genomic.fna/target_genomes.txt --output GCF_025994515.1_ASM2599451v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:33,249] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:33,249] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg72316e02-173b-46f5-a8bf-b1814f13da70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:33,250] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg72316e02-173b-46f5-a8bf-b1814f13da70/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:33,264] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:51:33,264] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:33,264] [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 rhaeticus	strain=LMG 22126	GCA_003207855.1	215221	215221	type	True	99.9995	1082	1082	95	conclusive
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	85.9431	780	1082	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	85.8522	787	1082	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	85.6809	765	1082	95	below_threshold
Komagataeibacter xylinus	strain=NBRC 15237	GCA_001571345.1	28448	28448	suspected-type	True	85.4884	756	1082	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	85.3103	758	1082	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	85.2425	768	1082	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	85.2053	759	1082	95	below_threshold
Komagataeibacter intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	85.0782	777	1082	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	84.8088	773	1082	95	below_threshold
Komagataeibacter kakiaceti	strain=JCM 25156	GCA_000613305.1	943261	943261	type	True	84.5097	345	1082	95	below_threshold
Komagataeibacter saccharivorans	strain=LMG 1582	GCA_003207825.1	265959	265959	type	True	84.1613	682	1082	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.0285	360	1082	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.2655	117	1082	95	below_threshold
Hoeflea alexandrii	strain=DSM 16655	GCA_024105735.1	288436	288436	type	True	76.0437	55	1082	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.8619	61	1082	95	below_threshold
Bradyrhizobium elkanii	strain=USDA 76	GCA_023278185.1	29448	29448	type	True	75.7888	79	1082	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:33,266] [INFO] DFAST Taxonomy check result was written to GCF_025994515.1_ASM2599451v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:33,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:33,270] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:33,270] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg72316e02-173b-46f5-a8bf-b1814f13da70/dqc_reference/checkm_data
[2024-01-24 11:51:33,271] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:33,310] [INFO] Task started: CheckM
[2024-01-24 11:51:33,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994515.1_ASM2599451v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994515.1_ASM2599451v1_genomic.fna/checkm_input GCF_025994515.1_ASM2599451v1_genomic.fna/checkm_result
[2024-01-24 11:52:10,741] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:10,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:10,766] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:10,766] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:10,767] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994515.1_ASM2599451v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:10,767] [INFO] Task started: Blastn
[2024-01-24 11:52:10,767] [INFO] Running command: blastn -query GCF_025994515.1_ASM2599451v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg72316e02-173b-46f5-a8bf-b1814f13da70/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994515.1_ASM2599451v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:12,260] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:12,266] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:12,266] [INFO] Target genome list was writen to GCF_025994515.1_ASM2599451v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:12,277] [INFO] Task started: fastANI
[2024-01-24 11:52:12,277] [INFO] Running command: fastANI --query /var/lib/cwl/stg5be220ac-c0f4-44b2-8578-fd57b64fc215/GCF_025994515.1_ASM2599451v1_genomic.fna.gz --refList GCF_025994515.1_ASM2599451v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994515.1_ASM2599451v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:23,395] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:23,409] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:23,409] [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_003207855.1	s__Komagataeibacter rhaeticus	99.9995	1082	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.08	98.72	0.93	0.91	8	conclusive
GCF_000182745.2	s__Komagataeibacter medellinensis	87.6372	824	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.49	98.49	0.84	0.84	2	-
GCF_000285295.1	s__Komagataeibacter europaeus	85.9376	780	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_003207895.1	s__Komagataeibacter swingsii	85.8634	786	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_004302915.1	s__Komagataeibacter xylinus_C	85.747	796	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015155755.1	s__Komagataeibacter sp015155755	85.4913	733	1082	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	85.3245	757	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003207815.1	s__Komagataeibacter oboediens	85.2425	768	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.65	98.22	0.88	0.85	10	-
GCF_003207795.1	s__Komagataeibacter nataicola	85.1859	760	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.90	99.90	0.97	0.97	2	-
GCF_009834365.1	s__Komagataeibacter xylinus_D	85.1164	774	1082	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	85.0782	777	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_006538165.1	s__Komagataeibacter diospyri	84.8088	773	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
GCF_014199155.1	s__Komagataeibacter kakiaceti	84.7647	715	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_003207825.1	s__Komagataeibacter saccharivorans	84.1369	684	1082	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.47	98.42	0.92	0.87	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:23,411] [INFO] GTDB search result was written to GCF_025994515.1_ASM2599451v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:23,412] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:23,416] [INFO] DFAST_QC result json was written to GCF_025994515.1_ASM2599451v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:23,416] [INFO] DFAST_QC completed!
[2024-01-24 11:52:23,416] [INFO] Total running time: 0h1m17s