[2024-01-24 15:18:05,087] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:05,090] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:05,090] [INFO] DQC Reference Directory: /var/lib/cwl/stg76658b5a-5fc5-42ca-a125-c1041c784ca3/dqc_reference
[2024-01-24 15:18:07,532] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:07,533] [INFO] Task started: Prodigal
[2024-01-24 15:18:07,534] [INFO] Running command: gunzip -c /var/lib/cwl/stgbf8d1ac8-9261-46a2-9e5e-1aecdcd3d80c/GCF_025994555.1_ASM2599455v1_genomic.fna.gz | prodigal -d GCF_025994555.1_ASM2599455v1_genomic.fna/cds.fna -a GCF_025994555.1_ASM2599455v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:17,963] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:17,964] [INFO] Task started: HMMsearch
[2024-01-24 15:18:17,964] [INFO] Running command: hmmsearch --tblout GCF_025994555.1_ASM2599455v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg76658b5a-5fc5-42ca-a125-c1041c784ca3/dqc_reference/reference_markers.hmm GCF_025994555.1_ASM2599455v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:18,266] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:18,268] [INFO] Found 6/6 markers.
[2024-01-24 15:18:18,303] [INFO] Query marker FASTA was written to GCF_025994555.1_ASM2599455v1_genomic.fna/markers.fasta
[2024-01-24 15:18:18,303] [INFO] Task started: Blastn
[2024-01-24 15:18:18,303] [INFO] Running command: blastn -query GCF_025994555.1_ASM2599455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76658b5a-5fc5-42ca-a125-c1041c784ca3/dqc_reference/reference_markers.fasta -out GCF_025994555.1_ASM2599455v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:19,155] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:19,159] [INFO] Selected 17 target genomes.
[2024-01-24 15:18:19,160] [INFO] Target genome list was writen to GCF_025994555.1_ASM2599455v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:19,250] [INFO] Task started: fastANI
[2024-01-24 15:18:19,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8d1ac8-9261-46a2-9e5e-1aecdcd3d80c/GCF_025994555.1_ASM2599455v1_genomic.fna.gz --refList GCF_025994555.1_ASM2599455v1_genomic.fna/target_genomes.txt --output GCF_025994555.1_ASM2599455v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:31,631] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:31,632] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg76658b5a-5fc5-42ca-a125-c1041c784ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:31,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg76658b5a-5fc5-42ca-a125-c1041c784ca3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:31,650] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:18:31,651] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:31,651] [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 saccharivorans	strain=LMG 1582	GCA_003207825.1	265959	265959	type	True	99.9965	1034	1041	95	conclusive
Komagataeibacter melaceti	strain=AV382	GCA_003403295.1	2766577	2766577	type	True	85.1778	714	1041	95	below_threshold
Komagataeibacter intermedius	strain=TF2	GCA_000964425.1	66229	66229	type	True	84.8281	723	1041	95	below_threshold
Komagataeibacter kakiaceti	strain=JCM 25156	GCA_000613305.1	943261	943261	type	True	84.6829	358	1041	95	below_threshold
Komagataeibacter swingsii	strain=LMG 22125	GCA_003207895.1	215220	215220	type	True	84.6441	728	1041	95	below_threshold
Komagataeibacter europaeus	strain=type strain:LMG 18890	GCA_000285295.1	33995	33995	suspected-type	True	84.6217	744	1041	95	below_threshold
Komagataeibacter diospyri	strain=MSKU 9	GCA_006538165.1	1932662	1932662	type	True	84.5108	742	1041	95	below_threshold
Komagataeibacter oboediens	strain=LMG 18849	GCA_003207815.1	65958	65958	type	True	84.3988	714	1041	95	below_threshold
Komagataeibacter rhaeticus	strain=LMG 22126	GCA_003207855.1	215221	215221	type	True	83.9769	714	1041	95	below_threshold
Komagataeibacter melomenusus	strain=AV436	GCA_013155395.1	2766578	2766578	type	True	83.6392	689	1041	95	below_threshold
Komagataeibacter sucrofermentans	strain=LMG 18788	GCA_003207865.1	1053551	1053551	type	True	83.5661	685	1041	95	below_threshold
Komagataeibacter nataicola	strain=LMG 1536	GCA_003207795.1	265960	265960	type	True	83.4148	683	1041	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	79.2074	331	1041	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.6844	168	1041	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.3671	140	1041	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.5425	102	1041	95	below_threshold
Azospirillum cavernae	strain=K2W22B-5	GCA_003590795.1	2320860	2320860	type	True	75.6638	87	1041	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:31,653] [INFO] DFAST Taxonomy check result was written to GCF_025994555.1_ASM2599455v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:31,653] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:31,653] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:31,654] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg76658b5a-5fc5-42ca-a125-c1041c784ca3/dqc_reference/checkm_data
[2024-01-24 15:18:31,655] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:31,688] [INFO] Task started: CheckM
[2024-01-24 15:18:31,688] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025994555.1_ASM2599455v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025994555.1_ASM2599455v1_genomic.fna/checkm_input GCF_025994555.1_ASM2599455v1_genomic.fna/checkm_result
[2024-01-24 15:19:06,797] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:06,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:06,846] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:06,847] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:06,847] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025994555.1_ASM2599455v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:06,847] [INFO] Task started: Blastn
[2024-01-24 15:19:06,848] [INFO] Running command: blastn -query GCF_025994555.1_ASM2599455v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg76658b5a-5fc5-42ca-a125-c1041c784ca3/dqc_reference/reference_markers_gtdb.fasta -out GCF_025994555.1_ASM2599455v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:08,270] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:08,278] [INFO] Selected 13 target genomes.
[2024-01-24 15:19:08,278] [INFO] Target genome list was writen to GCF_025994555.1_ASM2599455v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:08,288] [INFO] Task started: fastANI
[2024-01-24 15:19:08,288] [INFO] Running command: fastANI --query /var/lib/cwl/stgbf8d1ac8-9261-46a2-9e5e-1aecdcd3d80c/GCF_025994555.1_ASM2599455v1_genomic.fna.gz --refList GCF_025994555.1_ASM2599455v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025994555.1_ASM2599455v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:18,910] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:18,926] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:18,927] [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_003207825.1	s__Komagataeibacter saccharivorans	99.9965	1034	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.47	98.42	0.92	0.87	4	conclusive
GCF_003403295.1	s__Komagataeibacter melaceti	85.1871	713	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014199155.1	s__Komagataeibacter kakiaceti	85.1489	745	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_000964425.1	s__Komagataeibacter intermedius	84.8391	722	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_003207895.1	s__Komagataeibacter swingsii	84.6441	728	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_000285295.1	s__Komagataeibacter europaeus	84.5871	746	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_006538165.1	s__Komagataeibacter diospyri	84.4972	743	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.62	98.62	0.92	0.92	2	-
GCF_003207815.1	s__Komagataeibacter oboediens	84.4128	713	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.65	98.22	0.88	0.85	10	-
GCF_003207855.1	s__Komagataeibacter rhaeticus	84.0045	711	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.08	98.72	0.93	0.91	8	-
GCF_013155395.1	s__Komagataeibacter melomenusus	83.6392	689	1041	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	83.5528	686	1041	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	83.4081	684	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.90	99.90	0.97	0.97	2	-
GCF_000182745.2	s__Komagataeibacter medellinensis	82.9786	690	1041	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.49	98.49	0.84	0.84	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:18,928] [INFO] GTDB search result was written to GCF_025994555.1_ASM2599455v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:18,929] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:18,933] [INFO] DFAST_QC result json was written to GCF_025994555.1_ASM2599455v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:18,933] [INFO] DFAST_QC completed!
[2024-01-24 15:19:18,933] [INFO] Total running time: 0h1m14s