[2024-01-24 11:02:48,560] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:02:48,562] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:02:48,563] [INFO] DQC Reference Directory: /var/lib/cwl/stgc9d6199f-4989-48e9-bbfa-d655210b86df/dqc_reference
[2024-01-24 11:02:49,753] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:02:49,754] [INFO] Task started: Prodigal
[2024-01-24 11:02:49,754] [INFO] Running command: gunzip -c /var/lib/cwl/stgddf3acc9-f11b-40fc-8e70-92ed0f5ec48c/GCF_003206475.1_ASM320647v1_genomic.fna.gz | prodigal -d GCF_003206475.1_ASM320647v1_genomic.fna/cds.fna -a GCF_003206475.1_ASM320647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:03:01,304] [INFO] Task succeeded: Prodigal
[2024-01-24 11:03:01,304] [INFO] Task started: HMMsearch
[2024-01-24 11:03:01,305] [INFO] Running command: hmmsearch --tblout GCF_003206475.1_ASM320647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc9d6199f-4989-48e9-bbfa-d655210b86df/dqc_reference/reference_markers.hmm GCF_003206475.1_ASM320647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:03:01,586] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:03:01,587] [INFO] Found 6/6 markers.
[2024-01-24 11:03:01,621] [INFO] Query marker FASTA was written to GCF_003206475.1_ASM320647v1_genomic.fna/markers.fasta
[2024-01-24 11:03:01,621] [INFO] Task started: Blastn
[2024-01-24 11:03:01,621] [INFO] Running command: blastn -query GCF_003206475.1_ASM320647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d6199f-4989-48e9-bbfa-d655210b86df/dqc_reference/reference_markers.fasta -out GCF_003206475.1_ASM320647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:02,486] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:02,490] [INFO] Selected 11 target genomes.
[2024-01-24 11:03:02,491] [INFO] Target genome list was writen to GCF_003206475.1_ASM320647v1_genomic.fna/target_genomes.txt
[2024-01-24 11:03:02,510] [INFO] Task started: fastANI
[2024-01-24 11:03:02,510] [INFO] Running command: fastANI --query /var/lib/cwl/stgddf3acc9-f11b-40fc-8e70-92ed0f5ec48c/GCF_003206475.1_ASM320647v1_genomic.fna.gz --refList GCF_003206475.1_ASM320647v1_genomic.fna/target_genomes.txt --output GCF_003206475.1_ASM320647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:03:10,855] [INFO] Task succeeded: fastANI
[2024-01-24 11:03:10,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc9d6199f-4989-48e9-bbfa-d655210b86df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:03:10,857] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc9d6199f-4989-48e9-bbfa-d655210b86df/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:03:10,872] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:03:10,872] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:03:10,872] [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_003206475.1	1203393	1203393	type	True	100.0	1150	1156	95	conclusive
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	99.967	1112	1156	95	conclusive
Novacetimonas hansenii	strain=NBRC 14820	GCA_006539705.1	436	436	type	True	87.0447	785	1156	95	below_threshold
Novacetimonas hansenii	strain=JCM 7643	GCA_000964405.1	436	436	type	True	86.9273	766	1156	95	below_threshold
Novacetimonas pomaceti	strain=T5K1	GCA_003207955.1	2021998	2021998	type	True	86.589	843	1156	95	below_threshold
Novacetimonas cocois	strain=WE7	GCA_003311635.1	1747507	1747507	type	True	86.3136	858	1156	95	below_threshold
Roseomonas haemaphysalidis	strain=546	GCA_017355405.1	2768162	2768162	type	True	76.7329	157	1156	95	below_threshold
Acidiphilium iwatense	strain=KCTC 23505	GCA_021556475.1	768198	768198	type	True	76.382	109	1156	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_022953075.1	1582356	1582356	type	True	75.8868	55	1156	95	below_threshold
Sphingomicrobium aestuariivivum	strain=KCTC 42286	GCA_024721585.1	1582356	1582356	type	True	75.8424	52	1156	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.6122	62	1156	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:03:10,874] [INFO] DFAST Taxonomy check result was written to GCF_003206475.1_ASM320647v1_genomic.fna/tc_result.tsv
[2024-01-24 11:03:10,874] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:03:10,875] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:03:10,875] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc9d6199f-4989-48e9-bbfa-d655210b86df/dqc_reference/checkm_data
[2024-01-24 11:03:10,876] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:03:10,911] [INFO] Task started: CheckM
[2024-01-24 11:03:10,911] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003206475.1_ASM320647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003206475.1_ASM320647v1_genomic.fna/checkm_input GCF_003206475.1_ASM320647v1_genomic.fna/checkm_result
[2024-01-24 11:03:52,040] [INFO] Task succeeded: CheckM
[2024-01-24 11:03:52,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:03:52,069] [INFO] ===== Completeness check finished =====
[2024-01-24 11:03:52,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:03:52,070] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003206475.1_ASM320647v1_genomic.fna/markers.fasta)
[2024-01-24 11:03:52,070] [INFO] Task started: Blastn
[2024-01-24 11:03:52,070] [INFO] Running command: blastn -query GCF_003206475.1_ASM320647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc9d6199f-4989-48e9-bbfa-d655210b86df/dqc_reference/reference_markers_gtdb.fasta -out GCF_003206475.1_ASM320647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:03:53,602] [INFO] Task succeeded: Blastn
[2024-01-24 11:03:53,607] [INFO] Selected 9 target genomes.
[2024-01-24 11:03:53,607] [INFO] Target genome list was writen to GCF_003206475.1_ASM320647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:03:53,616] [INFO] Task started: fastANI
[2024-01-24 11:03:53,616] [INFO] Running command: fastANI --query /var/lib/cwl/stgddf3acc9-f11b-40fc-8e70-92ed0f5ec48c/GCF_003206475.1_ASM320647v1_genomic.fna.gz --refList GCF_003206475.1_ASM320647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003206475.1_ASM320647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:04:01,893] [INFO] Task succeeded: fastANI
[2024-01-24 11:04:01,910] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:04:01,911] [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	99.967	1112	1156	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	92.4818	953	1156	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	86.9115	767	1156	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	86.286	860	1156	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	82.7734	659	1156	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	81.8403	602	1156	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	81.6399	600	1156	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	79.6693	474	1156	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	79.3912	435	1156	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 11:04:01,913] [INFO] GTDB search result was written to GCF_003206475.1_ASM320647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:04:01,913] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:04:01,918] [INFO] DFAST_QC result json was written to GCF_003206475.1_ASM320647v1_genomic.fna/dqc_result.json
[2024-01-24 11:04:01,918] [INFO] DFAST_QC completed!
[2024-01-24 11:04:01,918] [INFO] Total running time: 0h1m13s