[2024-01-24 15:18:27,021] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:27,030] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:27,030] [INFO] DQC Reference Directory: /var/lib/cwl/stgeeea98de-0c28-43b7-936e-0da52cc26c84/dqc_reference
[2024-01-24 15:18:28,540] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:28,541] [INFO] Task started: Prodigal
[2024-01-24 15:18:28,541] [INFO] Running command: gunzip -c /var/lib/cwl/stgce85a2f4-e21d-4212-9b3f-82a45a09af3e/GCF_002906255.1_ASM290625v1_genomic.fna.gz | prodigal -d GCF_002906255.1_ASM290625v1_genomic.fna/cds.fna -a GCF_002906255.1_ASM290625v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:40,730] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:40,730] [INFO] Task started: HMMsearch
[2024-01-24 15:18:40,730] [INFO] Running command: hmmsearch --tblout GCF_002906255.1_ASM290625v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgeeea98de-0c28-43b7-936e-0da52cc26c84/dqc_reference/reference_markers.hmm GCF_002906255.1_ASM290625v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:41,085] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:41,086] [INFO] Found 6/6 markers.
[2024-01-24 15:18:41,120] [INFO] Query marker FASTA was written to GCF_002906255.1_ASM290625v1_genomic.fna/markers.fasta
[2024-01-24 15:18:41,120] [INFO] Task started: Blastn
[2024-01-24 15:18:41,120] [INFO] Running command: blastn -query GCF_002906255.1_ASM290625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeea98de-0c28-43b7-936e-0da52cc26c84/dqc_reference/reference_markers.fasta -out GCF_002906255.1_ASM290625v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:42,019] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:42,022] [INFO] Selected 11 target genomes.
[2024-01-24 15:18:42,022] [INFO] Target genome list was writen to GCF_002906255.1_ASM290625v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:42,027] [INFO] Task started: fastANI
[2024-01-24 15:18:42,027] [INFO] Running command: fastANI --query /var/lib/cwl/stgce85a2f4-e21d-4212-9b3f-82a45a09af3e/GCF_002906255.1_ASM290625v1_genomic.fna.gz --refList GCF_002906255.1_ASM290625v1_genomic.fna/target_genomes.txt --output GCF_002906255.1_ASM290625v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:50,653] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:50,653] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgeeea98de-0c28-43b7-936e-0da52cc26c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:50,653] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgeeea98de-0c28-43b7-936e-0da52cc26c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:50,662] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:18:50,663] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:18:50,663] [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
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	100.0	1130	1136	95	conclusive
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	99.9896	1107	1136	95	conclusive
Novacetimonas hansenii	strain=NBRC 14820	GCA_006539705.1	436	436	type	True	86.8317	782	1136	95	below_threshold
Novacetimonas hansenii	strain=JCM 7643	GCA_000964405.1	436	436	type	True	86.83	745	1136	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	86.6001	833	1136	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	86.3511	827	1136	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.7706	157	1136	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.5241	105	1136	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.8606	55	1136	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:50,665] [INFO] DFAST Taxonomy check result was written to GCF_002906255.1_ASM290625v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:50,665] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:50,665] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:50,666] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgeeea98de-0c28-43b7-936e-0da52cc26c84/dqc_reference/checkm_data
[2024-01-24 15:18:50,667] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:50,708] [INFO] Task started: CheckM
[2024-01-24 15:18:50,708] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002906255.1_ASM290625v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002906255.1_ASM290625v1_genomic.fna/checkm_input GCF_002906255.1_ASM290625v1_genomic.fna/checkm_result
[2024-01-24 15:19:33,105] [INFO] Task succeeded: CheckM
[2024-01-24 15:19:33,107] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:19:33,125] [INFO] ===== Completeness check finished =====
[2024-01-24 15:19:33,126] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:19:33,126] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002906255.1_ASM290625v1_genomic.fna/markers.fasta)
[2024-01-24 15:19:33,126] [INFO] Task started: Blastn
[2024-01-24 15:19:33,127] [INFO] Running command: blastn -query GCF_002906255.1_ASM290625v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgeeea98de-0c28-43b7-936e-0da52cc26c84/dqc_reference/reference_markers_gtdb.fasta -out GCF_002906255.1_ASM290625v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:19:34,743] [INFO] Task succeeded: Blastn
[2024-01-24 15:19:34,748] [INFO] Selected 9 target genomes.
[2024-01-24 15:19:34,748] [INFO] Target genome list was writen to GCF_002906255.1_ASM290625v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:19:34,757] [INFO] Task started: fastANI
[2024-01-24 15:19:34,757] [INFO] Running command: fastANI --query /var/lib/cwl/stgce85a2f4-e21d-4212-9b3f-82a45a09af3e/GCF_002906255.1_ASM290625v1_genomic.fna.gz --refList GCF_002906255.1_ASM290625v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002906255.1_ASM290625v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:19:43,225] [INFO] Task succeeded: fastANI
[2024-01-24 15:19:43,236] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:19:43,237] [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_002906255.1	s__Komagataeibacter maltaceti	100.0	1130	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.99	99.99	0.97	0.97	2	conclusive
GCF_003206495.1	s__Komagataeibacter entanii	92.5266	928	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.26	98.23	0.88	0.87	3	-
GCF_000964405.1	s__Komagataeibacter hansenii	86.8168	746	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.02	97.76	0.88	0.75	12	-
GCF_003311635.1	s__Komagataeibacter cocois	86.3436	827	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	95.20	95.16	0.89	0.89	4	-
GCF_003207895.1	s__Komagataeibacter swingsii	82.7418	652	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	96.10	95.69	0.87	0.84	5	-
GCF_014199155.1	s__Komagataeibacter kakiaceti	81.8497	593	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.94	99.94	1.00	1.00	2	-
GCF_003207855.1	s__Komagataeibacter rhaeticus	81.4688	595	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.08	98.72	0.93	0.91	8	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	79.8233	459	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174395.1	s__Gluconacetobacter aggeris	79.4602	423	1136	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:19:43,239] [INFO] GTDB search result was written to GCF_002906255.1_ASM290625v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:19:43,239] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:19:43,243] [INFO] DFAST_QC result json was written to GCF_002906255.1_ASM290625v1_genomic.fna/dqc_result.json
[2024-01-24 15:19:43,244] [INFO] DFAST_QC completed!
[2024-01-24 15:19:43,244] [INFO] Total running time: 0h1m16s