[2024-01-24 12:42:05,170] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:42:05,172] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:42:05,172] [INFO] DQC Reference Directory: /var/lib/cwl/stgabbccaa4-54c5-435e-a97c-de2bce461ecc/dqc_reference
[2024-01-24 12:42:06,417] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:42:06,418] [INFO] Task started: Prodigal
[2024-01-24 12:42:06,419] [INFO] Running command: gunzip -c /var/lib/cwl/stgbc73208e-5900-4cf1-b144-953905a6cc3f/GCF_006539705.1_ASM653970v1_genomic.fna.gz | prodigal -d GCF_006539705.1_ASM653970v1_genomic.fna/cds.fna -a GCF_006539705.1_ASM653970v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:42:17,947] [INFO] Task succeeded: Prodigal
[2024-01-24 12:42:17,948] [INFO] Task started: HMMsearch
[2024-01-24 12:42:17,948] [INFO] Running command: hmmsearch --tblout GCF_006539705.1_ASM653970v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgabbccaa4-54c5-435e-a97c-de2bce461ecc/dqc_reference/reference_markers.hmm GCF_006539705.1_ASM653970v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:42:18,217] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:42:18,218] [INFO] Found 6/6 markers.
[2024-01-24 12:42:18,256] [INFO] Query marker FASTA was written to GCF_006539705.1_ASM653970v1_genomic.fna/markers.fasta
[2024-01-24 12:42:18,257] [INFO] Task started: Blastn
[2024-01-24 12:42:18,257] [INFO] Running command: blastn -query GCF_006539705.1_ASM653970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabbccaa4-54c5-435e-a97c-de2bce461ecc/dqc_reference/reference_markers.fasta -out GCF_006539705.1_ASM653970v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:42:19,046] [INFO] Task succeeded: Blastn
[2024-01-24 12:42:19,049] [INFO] Selected 12 target genomes.
[2024-01-24 12:42:19,050] [INFO] Target genome list was writen to GCF_006539705.1_ASM653970v1_genomic.fna/target_genomes.txt
[2024-01-24 12:42:19,067] [INFO] Task started: fastANI
[2024-01-24 12:42:19,067] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc73208e-5900-4cf1-b144-953905a6cc3f/GCF_006539705.1_ASM653970v1_genomic.fna.gz --refList GCF_006539705.1_ASM653970v1_genomic.fna/target_genomes.txt --output GCF_006539705.1_ASM653970v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:42:28,016] [INFO] Task succeeded: fastANI
[2024-01-24 12:42:28,016] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgabbccaa4-54c5-435e-a97c-de2bce461ecc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:42:28,016] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgabbccaa4-54c5-435e-a97c-de2bce461ecc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:42:28,025] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:42:28,025] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:42:28,026] [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=NBRC 14820	GCA_006539705.1	436	436	type	True	100.0	1093	1104	95	conclusive
Novacetimonas hansenii	strain=JCM 7643	GCA_000964405.1	436	436	type	True	99.9252	1036	1104	95	conclusive
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	86.939	799	1104	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	86.9194	786	1104	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	84.376	705	1104	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	84.353	709	1104	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	79.1518	327	1104	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	76.6021	112	1104	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.5585	87	1104	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:42:28,027] [INFO] DFAST Taxonomy check result was written to GCF_006539705.1_ASM653970v1_genomic.fna/tc_result.tsv
[2024-01-24 12:42:28,028] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:42:28,029] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:42:28,029] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgabbccaa4-54c5-435e-a97c-de2bce461ecc/dqc_reference/checkm_data
[2024-01-24 12:42:28,031] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:42:28,075] [INFO] Task started: CheckM
[2024-01-24 12:42:28,075] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539705.1_ASM653970v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539705.1_ASM653970v1_genomic.fna/checkm_input GCF_006539705.1_ASM653970v1_genomic.fna/checkm_result
[2024-01-24 12:43:06,531] [INFO] Task succeeded: CheckM
[2024-01-24 12:43:06,533] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:43:06,556] [INFO] ===== Completeness check finished =====
[2024-01-24 12:43:06,557] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:43:06,557] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539705.1_ASM653970v1_genomic.fna/markers.fasta)
[2024-01-24 12:43:06,557] [INFO] Task started: Blastn
[2024-01-24 12:43:06,558] [INFO] Running command: blastn -query GCF_006539705.1_ASM653970v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgabbccaa4-54c5-435e-a97c-de2bce461ecc/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539705.1_ASM653970v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:43:07,875] [INFO] Task succeeded: Blastn
[2024-01-24 12:43:07,879] [INFO] Selected 11 target genomes.
[2024-01-24 12:43:07,879] [INFO] Target genome list was writen to GCF_006539705.1_ASM653970v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:43:07,887] [INFO] Task started: fastANI
[2024-01-24 12:43:07,887] [INFO] Running command: fastANI --query /var/lib/cwl/stgbc73208e-5900-4cf1-b144-953905a6cc3f/GCF_006539705.1_ASM653970v1_genomic.fna.gz --refList GCF_006539705.1_ASM653970v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539705.1_ASM653970v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:43:16,397] [INFO] Task succeeded: fastANI
[2024-01-24 12:43:16,412] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:43:16,413] [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	99.9252	1036	1104	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	87.2586	788	1104	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	86.9194	786	1104	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	84.3744	705	1104	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	80.7774	515	1104	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	80.5359	474	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.80	99.80	0.96	0.96	2	-
GCF_003207855.1	s__Komagataeibacter rhaeticus	79.9921	473	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.08	98.72	0.93	0.91	8	-
GCF_003403295.1	s__Komagataeibacter melaceti	79.9564	439	1104	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	79.1442	328	1104	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	78.9267	329	1104	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	78.5193	331	1104	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 12:43:16,415] [INFO] GTDB search result was written to GCF_006539705.1_ASM653970v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:43:16,416] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:43:16,421] [INFO] DFAST_QC result json was written to GCF_006539705.1_ASM653970v1_genomic.fna/dqc_result.json
[2024-01-24 12:43:16,422] [INFO] DFAST_QC completed!
[2024-01-24 12:43:16,422] [INFO] Total running time: 0h1m11s