[2023-06-27 18:43:31,351] [INFO] DFAST_QC pipeline started.
[2023-06-27 18:43:31,353] [INFO] DFAST_QC version: 0.5.7
[2023-06-27 18:43:31,353] [INFO] DQC Reference Directory: /var/lib/cwl/stgf700486c-dc5c-4af9-a44e-d1f63978051d/dqc_reference
[2023-06-27 18:43:32,579] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-27 18:43:32,580] [INFO] Task started: Prodigal
[2023-06-27 18:43:32,580] [INFO] Running command: gunzip -c /var/lib/cwl/stgfcd0e2c6-ec19-4735-bc33-fc0c69fdc260/GCA_002409655.1_ASM240965v1_genomic.fna.gz | prodigal -d GCA_002409655.1_ASM240965v1_genomic.fna/cds.fna -a GCA_002409655.1_ASM240965v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-27 18:43:40,457] [INFO] Task succeeded: Prodigal
[2023-06-27 18:43:40,458] [INFO] Task started: HMMsearch
[2023-06-27 18:43:40,458] [INFO] Running command: hmmsearch --tblout GCA_002409655.1_ASM240965v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf700486c-dc5c-4af9-a44e-d1f63978051d/dqc_reference/reference_markers.hmm GCA_002409655.1_ASM240965v1_genomic.fna/protein.faa > /dev/null
[2023-06-27 18:43:40,705] [INFO] Task succeeded: HMMsearch
[2023-06-27 18:43:40,707] [INFO] Found 6/6 markers.
[2023-06-27 18:43:40,734] [INFO] Query marker FASTA was written to GCA_002409655.1_ASM240965v1_genomic.fna/markers.fasta
[2023-06-27 18:43:40,734] [INFO] Task started: Blastn
[2023-06-27 18:43:40,734] [INFO] Running command: blastn -query GCA_002409655.1_ASM240965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf700486c-dc5c-4af9-a44e-d1f63978051d/dqc_reference/reference_markers.fasta -out GCA_002409655.1_ASM240965v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:43:41,347] [INFO] Task succeeded: Blastn
[2023-06-27 18:43:41,354] [INFO] Selected 11 target genomes.
[2023-06-27 18:43:41,355] [INFO] Target genome list was writen to GCA_002409655.1_ASM240965v1_genomic.fna/target_genomes.txt
[2023-06-27 18:43:41,363] [INFO] Task started: fastANI
[2023-06-27 18:43:41,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcd0e2c6-ec19-4735-bc33-fc0c69fdc260/GCA_002409655.1_ASM240965v1_genomic.fna.gz --refList GCA_002409655.1_ASM240965v1_genomic.fna/target_genomes.txt --output GCA_002409655.1_ASM240965v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-27 18:43:47,555] [INFO] Task succeeded: fastANI
[2023-06-27 18:43:47,556] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf700486c-dc5c-4af9-a44e-d1f63978051d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-27 18:43:47,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf700486c-dc5c-4af9-a44e-d1f63978051d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-27 18:43:47,575] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2023-06-27 18:43:47,575] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-27 18:43:47,576] [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
Acetobacter orientalis	strain=21F-2	GCA_000963965.1	146474	146474	type	True	97.8703	792	879	95	conclusive
Acetobacter orientalis	strain=NBRC 16606	GCA_007989335.1	146474	146474	type	True	97.8462	801	879	95	conclusive
Acetobacter cibinongensis	strain=4H-1	GCA_000963925.1	146475	146475	type	True	80.1863	413	879	95	below_threshold
Acetobacter cibinongensis	strain=NBRC 16605	GCA_007989305.1	146475	146475	type	True	80.0939	418	879	95	below_threshold
Acetobacter senegalensis	strain=LMG 23690	GCA_001580995.1	446692	446692	type	True	79.3401	325	879	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_007989245.1	104102	104102	type	True	79.0365	327	879	95	below_threshold
Acetobacter indonesiensis	strain=5H-1	GCA_000963945.1	104101	104101	type	True	78.9459	333	879	95	below_threshold
Acetobacter indonesiensis	strain=NBRC 16471	GCA_007991075.1	104101	104101	type	True	78.8857	344	879	95	below_threshold
Acetobacter orleanensis	strain=LMG 1583	GCA_001581005.1	104099	104099	type	True	78.4738	263	879	95	below_threshold
Acetobacter oryzoeni	strain=B6	GCA_004014775.2	2500548	2500548	type	True	77.9124	276	879	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-27 18:43:47,578] [INFO] DFAST Taxonomy check result was written to GCA_002409655.1_ASM240965v1_genomic.fna/tc_result.tsv
[2023-06-27 18:43:47,579] [INFO] ===== Taxonomy check completed =====
[2023-06-27 18:43:47,579] [INFO] ===== Start completeness check using CheckM =====
[2023-06-27 18:43:47,580] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf700486c-dc5c-4af9-a44e-d1f63978051d/dqc_reference/checkm_data
[2023-06-27 18:43:47,581] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-27 18:43:47,610] [INFO] Task started: CheckM
[2023-06-27 18:43:47,610] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_002409655.1_ASM240965v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_002409655.1_ASM240965v1_genomic.fna/checkm_input GCA_002409655.1_ASM240965v1_genomic.fna/checkm_result
[2023-06-27 18:44:14,832] [INFO] Task succeeded: CheckM
[2023-06-27 18:44:14,833] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-27 18:44:14,855] [INFO] ===== Completeness check finished =====
[2023-06-27 18:44:14,855] [INFO] ===== Start GTDB Search =====
[2023-06-27 18:44:14,856] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_002409655.1_ASM240965v1_genomic.fna/markers.fasta)
[2023-06-27 18:44:14,856] [INFO] Task started: Blastn
[2023-06-27 18:44:14,856] [INFO] Running command: blastn -query GCA_002409655.1_ASM240965v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf700486c-dc5c-4af9-a44e-d1f63978051d/dqc_reference/reference_markers_gtdb.fasta -out GCA_002409655.1_ASM240965v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-27 18:44:15,692] [INFO] Task succeeded: Blastn
[2023-06-27 18:44:15,697] [INFO] Selected 14 target genomes.
[2023-06-27 18:44:15,697] [INFO] Target genome list was writen to GCA_002409655.1_ASM240965v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-27 18:44:15,752] [INFO] Task started: fastANI
[2023-06-27 18:44:15,753] [INFO] Running command: fastANI --query /var/lib/cwl/stgfcd0e2c6-ec19-4735-bc33-fc0c69fdc260/GCA_002409655.1_ASM240965v1_genomic.fna.gz --refList GCA_002409655.1_ASM240965v1_genomic.fna/target_genomes_gtdb.txt --output GCA_002409655.1_ASM240965v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-27 18:44:24,074] [INFO] Task succeeded: fastANI
[2023-06-27 18:44:24,087] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-27 18:44:24,087] [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_000963965.1	s__Acetobacter orientalis	97.8703	792	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.55	97.80	0.92	0.88	7	conclusive
GCF_000963925.1	s__Acetobacter cibinongensis	80.1863	413	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.47	96.95	0.93	0.86	3	-
GCF_001580995.1	s__Acetobacter senegalensis	79.3449	325	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.25	96.97	0.85	0.80	6	-
GCF_001580915.1	s__Acetobacter tropicalis	79.0485	326	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.32	97.71	0.90	0.87	9	-
GCF_000963945.1	s__Acetobacter indonesiensis	78.9324	334	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	96.85	0.92	0.88	4	-
GCF_000613905.1	s__Acetobacter persici	78.7918	263	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
GCF_001580615.1	s__Acetobacter malorum	78.6609	270	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_001581005.1	s__Acetobacter orleanensis	78.4738	263	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	0.99	0.99	4	-
GCF_001580535.1	s__Acetobacter cerevisiae	78.2648	282	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.52	96.47	0.88	0.86	4	-
GCF_000723785.2	s__Acetobacter pasteurianus	77.9918	267	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.11	97.27	0.89	0.78	27	-
GCF_001499675.1	s__Acetobacter ghanensis	77.9876	229	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
GCF_004014775.2	s__Acetobacter oryzoeni	77.9124	276	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.72	97.29	0.89	0.84	4	-
GCF_001766235.1	s__Acetobacter ascendens	77.9055	244	879	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.38	98.13	0.85	0.83	6	-
--------------------------------------------------------------------------------
[2023-06-27 18:44:24,089] [INFO] GTDB search result was written to GCA_002409655.1_ASM240965v1_genomic.fna/result_gtdb.tsv
[2023-06-27 18:44:24,090] [INFO] ===== GTDB Search completed =====
[2023-06-27 18:44:24,093] [INFO] DFAST_QC result json was written to GCA_002409655.1_ASM240965v1_genomic.fna/dqc_result.json
[2023-06-27 18:44:24,094] [INFO] DFAST_QC completed!
[2023-06-27 18:44:24,094] [INFO] Total running time: 0h0m53s