[2024-01-24 15:02:23,441] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:23,445] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:23,446] [INFO] DQC Reference Directory: /var/lib/cwl/stg0bff57fe-b4bf-462f-a187-d5c274b4218a/dqc_reference
[2024-01-24 15:02:24,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:24,712] [INFO] Task started: Prodigal
[2024-01-24 15:02:24,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg8131c801-154c-42d3-8a3a-fe4074a00d19/GCF_000193495.2_ASM19349v2_genomic.fna.gz | prodigal -d GCF_000193495.2_ASM19349v2_genomic.fna/cds.fna -a GCF_000193495.2_ASM19349v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:35,524] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:35,524] [INFO] Task started: HMMsearch
[2024-01-24 15:02:35,524] [INFO] Running command: hmmsearch --tblout GCF_000193495.2_ASM19349v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0bff57fe-b4bf-462f-a187-d5c274b4218a/dqc_reference/reference_markers.hmm GCF_000193495.2_ASM19349v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:35,788] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:35,790] [INFO] Found 6/6 markers.
[2024-01-24 15:02:35,830] [INFO] Query marker FASTA was written to GCF_000193495.2_ASM19349v2_genomic.fna/markers.fasta
[2024-01-24 15:02:35,831] [INFO] Task started: Blastn
[2024-01-24 15:02:35,831] [INFO] Running command: blastn -query GCF_000193495.2_ASM19349v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bff57fe-b4bf-462f-a187-d5c274b4218a/dqc_reference/reference_markers.fasta -out GCF_000193495.2_ASM19349v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:36,647] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:36,652] [INFO] Selected 13 target genomes.
[2024-01-24 15:02:36,652] [INFO] Target genome list was writen to GCF_000193495.2_ASM19349v2_genomic.fna/target_genomes.txt
[2024-01-24 15:02:36,760] [INFO] Task started: fastANI
[2024-01-24 15:02:36,761] [INFO] Running command: fastANI --query /var/lib/cwl/stg8131c801-154c-42d3-8a3a-fe4074a00d19/GCF_000193495.2_ASM19349v2_genomic.fna.gz --refList GCF_000193495.2_ASM19349v2_genomic.fna/target_genomes.txt --output GCF_000193495.2_ASM19349v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:46,072] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:46,072] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0bff57fe-b4bf-462f-a187-d5c274b4218a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:46,073] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0bff57fe-b4bf-462f-a187-d5c274b4218a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:46,084] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 15:02:46,084] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:46,084] [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 aceti	strain=NBRC 14818	GCA_000193495.2	435	435	type	True	100.0	1226	1228	95	conclusive
Acetobacter aceti	strain=DSM 3508	GCA_004341595.1	435	435	type	True	99.978	1175	1228	95	conclusive
Acetobacter aceti	strain=NBRC 14818	GCA_000963905.1	435	435	type	True	99.9694	1119	1228	95	conclusive
Acetobacter conturbans	strain=LMG 1627	GCA_011516755.1	1737472	1737472	type	True	81.9345	562	1228	95	below_threshold
Acetobacter fallax	strain=LMG 1636	GCA_011516735.1	1737473	1737473	type	True	81.2437	326	1228	95	below_threshold
Acetobacter estunensis	strain=LMG 1626	GCA_011516945.1	104097	104097	type	True	80.1447	442	1228	95	below_threshold
Gluconobacter potus	strain=R-71646	GCA_015244705.1	2724927	2724927	type	True	79.8766	210	1228	95	below_threshold
Acetobacter indonesiensis	strain=NBRC 16471	GCA_007991075.1	104101	104101	type	True	78.8105	135	1228	95	below_threshold
Acetobacter indonesiensis	strain=5H-1	GCA_000963945.1	104101	104101	type	True	78.744	131	1228	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	78.1837	166	1228	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.2703	58	1228	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:46,086] [INFO] DFAST Taxonomy check result was written to GCF_000193495.2_ASM19349v2_genomic.fna/tc_result.tsv
[2024-01-24 15:02:46,086] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:46,086] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:46,087] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0bff57fe-b4bf-462f-a187-d5c274b4218a/dqc_reference/checkm_data
[2024-01-24 15:02:46,088] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:46,126] [INFO] Task started: CheckM
[2024-01-24 15:02:46,127] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000193495.2_ASM19349v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000193495.2_ASM19349v2_genomic.fna/checkm_input GCF_000193495.2_ASM19349v2_genomic.fna/checkm_result
[2024-01-24 15:03:24,993] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:24,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:25,013] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:25,014] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:25,014] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000193495.2_ASM19349v2_genomic.fna/markers.fasta)
[2024-01-24 15:03:25,015] [INFO] Task started: Blastn
[2024-01-24 15:03:25,015] [INFO] Running command: blastn -query GCF_000193495.2_ASM19349v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg0bff57fe-b4bf-462f-a187-d5c274b4218a/dqc_reference/reference_markers_gtdb.fasta -out GCF_000193495.2_ASM19349v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:26,479] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:26,482] [INFO] Selected 7 target genomes.
[2024-01-24 15:03:26,482] [INFO] Target genome list was writen to GCF_000193495.2_ASM19349v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:26,488] [INFO] Task started: fastANI
[2024-01-24 15:03:26,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg8131c801-154c-42d3-8a3a-fe4074a00d19/GCF_000193495.2_ASM19349v2_genomic.fna.gz --refList GCF_000193495.2_ASM19349v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000193495.2_ASM19349v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:33,781] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:33,789] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:33,789] [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_000193495.2	s__Acetobacter aceti	100.0	1225	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	98.82	96.47	0.96	0.89	7	conclusive
GCA_002409645.1	s__Acetobacter sp002409645	93.7249	978	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516765.1	s__Acetobacter sicerae	88.8512	992	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002005445.1	s__Acetobacter aceti_B	85.3754	916	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516755.1	s__Acetobacter conturbans	81.9345	562	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011516945.1	s__Acetobacter estunensis	80.1606	443	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	77.8165	196	1228	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:33,791] [INFO] GTDB search result was written to GCF_000193495.2_ASM19349v2_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:33,792] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:33,795] [INFO] DFAST_QC result json was written to GCF_000193495.2_ASM19349v2_genomic.fna/dqc_result.json
[2024-01-24 15:03:33,796] [INFO] DFAST_QC completed!
[2024-01-24 15:03:33,796] [INFO] Total running time: 0h1m10s