[2024-01-24 11:51:11,185] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:11,191] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:11,192] [INFO] DQC Reference Directory: /var/lib/cwl/stgf9fe7d3f-8c14-489f-bc83-8a177cce8f31/dqc_reference
[2024-01-24 11:51:12,416] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:12,423] [INFO] Task started: Prodigal
[2024-01-24 11:51:12,423] [INFO] Running command: gunzip -c /var/lib/cwl/stgc683f540-9664-46ad-aaa4-33ed4168d114/GCF_007989335.1_ASM798933v1_genomic.fna.gz | prodigal -d GCF_007989335.1_ASM798933v1_genomic.fna/cds.fna -a GCF_007989335.1_ASM798933v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:20,950] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:20,950] [INFO] Task started: HMMsearch
[2024-01-24 11:51:20,950] [INFO] Running command: hmmsearch --tblout GCF_007989335.1_ASM798933v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf9fe7d3f-8c14-489f-bc83-8a177cce8f31/dqc_reference/reference_markers.hmm GCF_007989335.1_ASM798933v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:21,221] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:21,222] [INFO] Found 6/6 markers.
[2024-01-24 11:51:21,264] [INFO] Query marker FASTA was written to GCF_007989335.1_ASM798933v1_genomic.fna/markers.fasta
[2024-01-24 11:51:21,264] [INFO] Task started: Blastn
[2024-01-24 11:51:21,264] [INFO] Running command: blastn -query GCF_007989335.1_ASM798933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9fe7d3f-8c14-489f-bc83-8a177cce8f31/dqc_reference/reference_markers.fasta -out GCF_007989335.1_ASM798933v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:21,975] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:21,979] [INFO] Selected 9 target genomes.
[2024-01-24 11:51:21,980] [INFO] Target genome list was writen to GCF_007989335.1_ASM798933v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:21,984] [INFO] Task started: fastANI
[2024-01-24 11:51:21,984] [INFO] Running command: fastANI --query /var/lib/cwl/stgc683f540-9664-46ad-aaa4-33ed4168d114/GCF_007989335.1_ASM798933v1_genomic.fna.gz --refList GCF_007989335.1_ASM798933v1_genomic.fna/target_genomes.txt --output GCF_007989335.1_ASM798933v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:27,868] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:27,869] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf9fe7d3f-8c14-489f-bc83-8a177cce8f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:27,869] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf9fe7d3f-8c14-489f-bc83-8a177cce8f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:27,879] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:51:27,879] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:27,879] [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=NBRC 16606	GCA_007989335.1	146474	146474	type	True	100.0	956	956	95	conclusive
Acetobacter orientalis	strain=21F-2	GCA_000963965.1	146474	146474	type	True	99.991	938	956	95	conclusive
Acetobacter cibinongensis	strain=4H-1	GCA_000963925.1	146475	146475	type	True	80.1532	432	956	95	below_threshold
Acetobacter cibinongensis	strain=NBRC 16605	GCA_007989305.1	146475	146475	type	True	80.1418	425	956	95	below_threshold
Acetobacter indonesiensis	strain=NBRC 16471	GCA_007991075.1	104101	104101	type	True	79.3778	343	956	95	below_threshold
Acetobacter indonesiensis	strain=5H-1	GCA_000963945.1	104101	104101	type	True	79.346	345	956	95	below_threshold
Acetobacter senegalensis	strain=LMG 23690	GCA_001580995.1	446692	446692	type	True	79.2762	341	956	95	below_threshold
Acetobacter tropicalis	strain=NBRC 16470	GCA_007989245.1	104102	104102	type	True	78.8251	322	956	95	below_threshold
Acetobacter ascendens	strain=LMG 1590	GCA_001766235.1	481146	481146	type	True	77.9886	254	956	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:27,881] [INFO] DFAST Taxonomy check result was written to GCF_007989335.1_ASM798933v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:27,882] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:27,882] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:27,882] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf9fe7d3f-8c14-489f-bc83-8a177cce8f31/dqc_reference/checkm_data
[2024-01-24 11:51:27,883] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:27,913] [INFO] Task started: CheckM
[2024-01-24 11:51:27,913] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989335.1_ASM798933v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989335.1_ASM798933v1_genomic.fna/checkm_input GCF_007989335.1_ASM798933v1_genomic.fna/checkm_result
[2024-01-24 11:51:56,145] [INFO] Task succeeded: CheckM
[2024-01-24 11:51:56,146] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:51:56,163] [INFO] ===== Completeness check finished =====
[2024-01-24 11:51:56,163] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:51:56,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989335.1_ASM798933v1_genomic.fna/markers.fasta)
[2024-01-24 11:51:56,164] [INFO] Task started: Blastn
[2024-01-24 11:51:56,164] [INFO] Running command: blastn -query GCF_007989335.1_ASM798933v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf9fe7d3f-8c14-489f-bc83-8a177cce8f31/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989335.1_ASM798933v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:57,265] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:57,269] [INFO] Selected 14 target genomes.
[2024-01-24 11:51:57,270] [INFO] Target genome list was writen to GCF_007989335.1_ASM798933v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:51:57,279] [INFO] Task started: fastANI
[2024-01-24 11:51:57,280] [INFO] Running command: fastANI --query /var/lib/cwl/stgc683f540-9664-46ad-aaa4-33ed4168d114/GCF_007989335.1_ASM798933v1_genomic.fna.gz --refList GCF_007989335.1_ASM798933v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989335.1_ASM798933v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:05,570] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:05,581] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:05,581] [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	99.991	938	956	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	80.1532	432	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.47	96.95	0.93	0.86	3	-
GCF_000963945.1	s__Acetobacter indonesiensis	79.346	345	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.28	96.85	0.92	0.88	4	-
GCF_001580995.1	s__Acetobacter senegalensis	79.2762	341	956	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	78.8462	327	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.32	97.71	0.90	0.87	9	-
GCF_001580615.1	s__Acetobacter malorum	78.6479	281	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	95.98	95.83	0.82	0.80	5	-
GCF_000613905.1	s__Acetobacter persici	78.5989	269	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	96.00	95.85	0.80	0.79	8	-
GCF_001580535.1	s__Acetobacter cerevisiae	78.5918	276	956	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	78.2443	259	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.11	97.27	0.89	0.78	27	-
GCF_002738225.1	s__Acetobacter pomorum	78.1214	229	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	97.71	97.71	0.83	0.83	2	-
GCF_004014775.2	s__Acetobacter oryzoeni	78.0592	275	956	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	77.9886	254	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.38	98.13	0.85	0.83	6	-
GCF_001499675.1	s__Acetobacter ghanensis	77.8605	243	956	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:05,583] [INFO] GTDB search result was written to GCF_007989335.1_ASM798933v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:05,584] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:05,587] [INFO] DFAST_QC result json was written to GCF_007989335.1_ASM798933v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:05,587] [INFO] DFAST_QC completed!
[2024-01-24 11:52:05,587] [INFO] Total running time: 0h0m54s