[2024-01-24 11:35:34,604] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:34,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:34,606] [INFO] DQC Reference Directory: /var/lib/cwl/stgba8d45a6-3445-46e7-835d-f8a10d3e8dd8/dqc_reference
[2024-01-24 11:35:35,827] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:35,827] [INFO] Task started: Prodigal
[2024-01-24 11:35:35,828] [INFO] Running command: gunzip -c /var/lib/cwl/stg23c57b63-16a5-4b8d-b6a5-8bd10e4441ce/GCF_025995235.1_ASM2599523v1_genomic.fna.gz | prodigal -d GCF_025995235.1_ASM2599523v1_genomic.fna/cds.fna -a GCF_025995235.1_ASM2599523v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:45,960] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:45,961] [INFO] Task started: HMMsearch
[2024-01-24 11:35:45,961] [INFO] Running command: hmmsearch --tblout GCF_025995235.1_ASM2599523v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgba8d45a6-3445-46e7-835d-f8a10d3e8dd8/dqc_reference/reference_markers.hmm GCF_025995235.1_ASM2599523v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:46,220] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:46,221] [INFO] Found 6/6 markers.
[2024-01-24 11:35:46,260] [INFO] Query marker FASTA was written to GCF_025995235.1_ASM2599523v1_genomic.fna/markers.fasta
[2024-01-24 11:35:46,260] [INFO] Task started: Blastn
[2024-01-24 11:35:46,261] [INFO] Running command: blastn -query GCF_025995235.1_ASM2599523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba8d45a6-3445-46e7-835d-f8a10d3e8dd8/dqc_reference/reference_markers.fasta -out GCF_025995235.1_ASM2599523v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:47,002] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:47,006] [INFO] Selected 20 target genomes.
[2024-01-24 11:35:47,007] [INFO] Target genome list was writen to GCF_025995235.1_ASM2599523v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:47,033] [INFO] Task started: fastANI
[2024-01-24 11:35:47,033] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c57b63-16a5-4b8d-b6a5-8bd10e4441ce/GCF_025995235.1_ASM2599523v1_genomic.fna.gz --refList GCF_025995235.1_ASM2599523v1_genomic.fna/target_genomes.txt --output GCF_025995235.1_ASM2599523v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:58,683] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:58,683] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgba8d45a6-3445-46e7-835d-f8a10d3e8dd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:58,684] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgba8d45a6-3445-46e7-835d-f8a10d3e8dd8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:58,703] [INFO] Found 20 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 11:35:58,703] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 11:35:58,703] [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
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	79.8609	394	1107	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	79.7911	400	1107	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	79.6346	387	1107	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	79.3759	369	1107	95	below_threshold
Gluconacetobacter liquefaciens	strain=NBRC 12388	GCA_006539085.1	89584	89584	type	True	78.8144	343	1107	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	78.8142	346	1107	95	below_threshold
Gluconacetobacter liquefaciens	strain=DSM 5603	GCA_003350405.1	89584	89584	type	True	78.7363	353	1107	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	78.057	219	1107	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_002906255.1	1203393	1203393	type	True	78.037	281	1107	95	below_threshold
Asaia siamensis	strain=CCM 7132	GCA_014635085.1	110479	110479	type	True	78.016	175	1107	95	below_threshold
Novacetimonas maltaceti	strain=LMG 1529	GCA_003206475.1	1203393	1203393	type	True	78.0099	286	1107	95	below_threshold
Acetobacter nitrogenifigens	strain=DSM 23921	GCA_000429165.1	285268	285268	type	True	77.9855	229	1107	95	below_threshold
Acetobacter nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	77.9271	224	1107	95	below_threshold
Asaia lannensis	strain=NBRC 102526	GCA_024054035.1	415421	415421	type	True	77.6761	160	1107	95	below_threshold
Gluconobacter aidae	strain=AC10	GCA_009547075.1	2662454	2662454	type	True	77.6487	179	1107	95	below_threshold
Asaia prunellae	strain=JCM 25354	GCA_000613885.1	610245	610245	type	True	77.4433	97	1107	95	below_threshold
Gluconobacter kondonii	strain=NBRC 3266	GCA_002723995.1	941463	941463	type	True	77.4117	167	1107	95	below_threshold
Gluconobacter cadivus	strain=LMG 1744	GCA_015244745.1	2728101	2728101	type	True	77.3325	162	1107	95	below_threshold
Rhodovarius lipocyclicus	strain=CCUG 44693	GCA_009900765.1	268410	268410	type	True	76.0674	142	1107	95	below_threshold
Novosphingobium percolationis	strain=c1	GCA_020179425.1	2871811	2871811	type	True	75.5307	64	1107	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:58,705] [INFO] DFAST Taxonomy check result was written to GCF_025995235.1_ASM2599523v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:58,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:58,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:58,706] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgba8d45a6-3445-46e7-835d-f8a10d3e8dd8/dqc_reference/checkm_data
[2024-01-24 11:35:58,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:58,742] [INFO] Task started: CheckM
[2024-01-24 11:35:58,743] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025995235.1_ASM2599523v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025995235.1_ASM2599523v1_genomic.fna/checkm_input GCF_025995235.1_ASM2599523v1_genomic.fna/checkm_result
[2024-01-24 11:36:31,922] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:31,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:31,944] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:31,944] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:31,944] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025995235.1_ASM2599523v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:31,945] [INFO] Task started: Blastn
[2024-01-24 11:36:31,945] [INFO] Running command: blastn -query GCF_025995235.1_ASM2599523v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgba8d45a6-3445-46e7-835d-f8a10d3e8dd8/dqc_reference/reference_markers_gtdb.fasta -out GCF_025995235.1_ASM2599523v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:33,099] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:33,103] [INFO] Selected 17 target genomes.
[2024-01-24 11:36:33,103] [INFO] Target genome list was writen to GCF_025995235.1_ASM2599523v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:33,116] [INFO] Task started: fastANI
[2024-01-24 11:36:33,116] [INFO] Running command: fastANI --query /var/lib/cwl/stg23c57b63-16a5-4b8d-b6a5-8bd10e4441ce/GCF_025995235.1_ASM2599523v1_genomic.fna.gz --refList GCF_025995235.1_ASM2599523v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025995235.1_ASM2599523v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:45,224] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:45,239] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:45,240] [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_013376175.1	s__Ameyamaea chiangmaiensis	99.8397	900	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Ameyamaea	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	79.8745	393	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174375.1	s__Gluconacetobacter asukensis	79.2416	373	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCF_014174215.1	s__Gluconacetobacter tumulicola	78.8017	362	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174275.1	s__Gluconacetobacter takamatsuzukensis	78.7601	398	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174305.1	s__Gluconacetobacter johannae	78.7311	376	1107	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	78.6385	366	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.2181	N/A	N/A	N/A	N/A	1	-
GCF_014174155.1	s__Gluconacetobacter tumulisoli	78.5492	383	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	78.503	367	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCF_014635085.1	s__Asaia siamensis	78.016	175	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Asaia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000429165.1	s__Acetobacter nitrogenifigens	77.9855	229	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acetobacter	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002723995.1	s__Gluconobacter kondonii	77.4117	167	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	97.23	97.04	0.89	0.87	8	-
GCF_015244745.1	s__Gluconobacter cadivus	77.3157	163	1107	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconobacter	95.0	96.53	96.31	0.92	0.90	5	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:45,241] [INFO] GTDB search result was written to GCF_025995235.1_ASM2599523v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:45,242] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:45,248] [INFO] DFAST_QC result json was written to GCF_025995235.1_ASM2599523v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:45,248] [INFO] DFAST_QC completed!
[2024-01-24 11:36:45,248] [INFO] Total running time: 0h1m11s