[2024-01-24 12:21:44,266] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,268] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,268] [INFO] DQC Reference Directory: /var/lib/cwl/stg6fe85025-ac05-4e9e-9d4d-eea46f82b217/dqc_reference
[2024-01-24 12:21:45,662] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,662] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,663] [INFO] Running command: gunzip -c /var/lib/cwl/stg50c2fc85-7031-4a0f-a0c7-26d6cf0ddea0/GCF_000964405.1_ASM96440v1_genomic.fna.gz | prodigal -d GCF_000964405.1_ASM96440v1_genomic.fna/cds.fna -a GCF_000964405.1_ASM96440v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:57,586] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:57,587] [INFO] Task started: HMMsearch
[2024-01-24 12:21:57,587] [INFO] Running command: hmmsearch --tblout GCF_000964405.1_ASM96440v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6fe85025-ac05-4e9e-9d4d-eea46f82b217/dqc_reference/reference_markers.hmm GCF_000964405.1_ASM96440v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:57,899] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:57,901] [INFO] Found 6/6 markers.
[2024-01-24 12:21:57,934] [INFO] Query marker FASTA was written to GCF_000964405.1_ASM96440v1_genomic.fna/markers.fasta
[2024-01-24 12:21:57,934] [INFO] Task started: Blastn
[2024-01-24 12:21:57,934] [INFO] Running command: blastn -query GCF_000964405.1_ASM96440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fe85025-ac05-4e9e-9d4d-eea46f82b217/dqc_reference/reference_markers.fasta -out GCF_000964405.1_ASM96440v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:58,774] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:58,779] [INFO] Selected 12 target genomes.
[2024-01-24 12:21:58,779] [INFO] Target genome list was writen to GCF_000964405.1_ASM96440v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:58,784] [INFO] Task started: fastANI
[2024-01-24 12:21:58,785] [INFO] Running command: fastANI --query /var/lib/cwl/stg50c2fc85-7031-4a0f-a0c7-26d6cf0ddea0/GCF_000964405.1_ASM96440v1_genomic.fna.gz --refList GCF_000964405.1_ASM96440v1_genomic.fna/target_genomes.txt --output GCF_000964405.1_ASM96440v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:08,139] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:08,139] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6fe85025-ac05-4e9e-9d4d-eea46f82b217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:08,140] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6fe85025-ac05-4e9e-9d4d-eea46f82b217/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:08,148] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:22:08,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:08,148] [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 hansenii	strain=JCM 7643	GCA_000964405.1	436	436	type	True	99.9999	1066	1076	95	conclusive
Novacetimonas hansenii	strain=NBRC 14820	GCA_006539705.1	436	436	type	True	99.9697	1006	1076	95	conclusive
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	86.8375	768	1076	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	86.8015	784	1076	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	84.4607	689	1076	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	84.3968	690	1076	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	79.0468	329	1076	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.4042	114	1076	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.3303	85	1076	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:22:08,150] [INFO] DFAST Taxonomy check result was written to GCF_000964405.1_ASM96440v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:08,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:08,151] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:08,151] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6fe85025-ac05-4e9e-9d4d-eea46f82b217/dqc_reference/checkm_data
[2024-01-24 12:22:08,152] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:08,197] [INFO] Task started: CheckM
[2024-01-24 12:22:08,198] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000964405.1_ASM96440v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000964405.1_ASM96440v1_genomic.fna/checkm_input GCF_000964405.1_ASM96440v1_genomic.fna/checkm_result
[2024-01-24 12:22:47,917] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:47,918] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:47,961] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:47,962] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:47,962] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000964405.1_ASM96440v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:47,962] [INFO] Task started: Blastn
[2024-01-24 12:22:47,962] [INFO] Running command: blastn -query GCF_000964405.1_ASM96440v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6fe85025-ac05-4e9e-9d4d-eea46f82b217/dqc_reference/reference_markers_gtdb.fasta -out GCF_000964405.1_ASM96440v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:49,366] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:49,370] [INFO] Selected 11 target genomes.
[2024-01-24 12:22:49,371] [INFO] Target genome list was writen to GCF_000964405.1_ASM96440v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:49,383] [INFO] Task started: fastANI
[2024-01-24 12:22:49,384] [INFO] Running command: fastANI --query /var/lib/cwl/stg50c2fc85-7031-4a0f-a0c7-26d6cf0ddea0/GCF_000964405.1_ASM96440v1_genomic.fna.gz --refList GCF_000964405.1_ASM96440v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000964405.1_ASM96440v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:57,976] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:57,986] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:57,987] [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_000964405.1	s__Komagataeibacter hansenii	99.9999	1066	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.02	97.76	0.88	0.75	12	conclusive
GCF_003206495.1	s__Komagataeibacter entanii	87.1738	778	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	98.26	98.23	0.88	0.87	3	-
GCF_002906255.1	s__Komagataeibacter maltaceti	86.8677	765	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.99	99.99	0.97	0.97	2	-
GCF_003311635.1	s__Komagataeibacter cocois	84.4607	689	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	95.20	95.16	0.89	0.89	4	-
GCF_000285295.1	s__Komagataeibacter europaeus	80.7009	506	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	97.91	97.46	0.85	0.81	8	-
GCF_000964425.1	s__Komagataeibacter intermedius	80.4833	462	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_003403295.1	s__Komagataeibacter melaceti	80.0236	434	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003207855.1	s__Komagataeibacter rhaeticus	79.9237	471	1076	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	79.0609	328	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174305.1	s__Gluconacetobacter johannae	78.8203	328	1076	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174395.1	s__Gluconacetobacter aggeris	78.4823	325	1076	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 12:22:57,988] [INFO] GTDB search result was written to GCF_000964405.1_ASM96440v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:57,989] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:57,992] [INFO] DFAST_QC result json was written to GCF_000964405.1_ASM96440v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:57,993] [INFO] DFAST_QC completed!
[2024-01-24 12:22:57,993] [INFO] Total running time: 0h1m14s