[2024-01-24 13:49:27,502] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:27,504] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:27,504] [INFO] DQC Reference Directory: /var/lib/cwl/stg7984919c-3c5a-4952-9ea9-4aff27eb21a6/dqc_reference
[2024-01-24 13:49:28,830] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:28,831] [INFO] Task started: Prodigal
[2024-01-24 13:49:28,832] [INFO] Running command: gunzip -c /var/lib/cwl/stgc2f63626-7060-40bf-b0e5-d604f956a4a0/GCF_026341395.1_ASM2634139v1_genomic.fna.gz | prodigal -d GCF_026341395.1_ASM2634139v1_genomic.fna/cds.fna -a GCF_026341395.1_ASM2634139v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:39,320] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:39,320] [INFO] Task started: HMMsearch
[2024-01-24 13:49:39,320] [INFO] Running command: hmmsearch --tblout GCF_026341395.1_ASM2634139v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7984919c-3c5a-4952-9ea9-4aff27eb21a6/dqc_reference/reference_markers.hmm GCF_026341395.1_ASM2634139v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:39,618] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:39,619] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgc2f63626-7060-40bf-b0e5-d604f956a4a0/GCF_026341395.1_ASM2634139v1_genomic.fna.gz]
[2024-01-24 13:49:39,652] [INFO] Query marker FASTA was written to GCF_026341395.1_ASM2634139v1_genomic.fna/markers.fasta
[2024-01-24 13:49:39,652] [INFO] Task started: Blastn
[2024-01-24 13:49:39,652] [INFO] Running command: blastn -query GCF_026341395.1_ASM2634139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7984919c-3c5a-4952-9ea9-4aff27eb21a6/dqc_reference/reference_markers.fasta -out GCF_026341395.1_ASM2634139v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:40,605] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:40,611] [INFO] Selected 18 target genomes.
[2024-01-24 13:49:40,611] [INFO] Target genome list was writen to GCF_026341395.1_ASM2634139v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:40,626] [INFO] Task started: fastANI
[2024-01-24 13:49:40,627] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2f63626-7060-40bf-b0e5-d604f956a4a0/GCF_026341395.1_ASM2634139v1_genomic.fna.gz --refList GCF_026341395.1_ASM2634139v1_genomic.fna/target_genomes.txt --output GCF_026341395.1_ASM2634139v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:54,178] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:54,179] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7984919c-3c5a-4952-9ea9-4aff27eb21a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:54,180] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7984919c-3c5a-4952-9ea9-4aff27eb21a6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:54,196] [INFO] Found 18 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:49:54,196] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:54,197] [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
Endobacter medicaginis	strain=CECT 8088	GCA_014192375.1	1181271	1181271	type	True	99.9838	1128	1152	95	conclusive
Endobacter medicaginis	strain=LMG 26838	GCA_013376135.1	1181271	1181271	type	True	99.5199	693	1152	95	conclusive
Acetobacter nitrogenifigens	strain=NBRC 105050	GCA_007991375.1	285268	285268	type	True	78.2005	152	1152	95	below_threshold
Acetobacter nitrogenifigens	strain=DSM 23921	GCA_000429165.1	285268	285268	type	True	78.1286	150	1152	95	below_threshold
Acidisphaera rubrifaciens	strain=HS-AP3	GCA_000964365.1	50715	50715	type	True	78.0837	216	1152	95	below_threshold
Gluconacetobacter dulcium	strain=LMG 1728	GCA_014174165.1	2729096	2729096	type	True	78.0622	312	1152	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5; ATCC 49037	GCA_000021325.1	33996	33996	type	True	77.9044	323	1152	95	below_threshold
Gluconacetobacter liquefaciens	strain=LMG 1382	GCA_014174285.1	89584	89584	type	True	77.8798	286	1152	95	below_threshold
Gluconacetobacter diazotrophicus	strain=LMG 7603	GCA_014174315.1	33996	33996	type	True	77.8584	314	1152	95	below_threshold
Gluconacetobacter diazotrophicus	strain=PAl 5	GCA_000067045.1	33996	33996	type	True	77.8416	331	1152	95	below_threshold
Rhodovastum atsumiense	strain=G2-11	GCA_937425535.1	504468	504468	type	True	77.7861	378	1152	95	below_threshold
Roseomonas cervicalis	strain=ATCC 49957	GCA_000164635.1	204525	204525	type	True	77.5307	305	1152	95	below_threshold
Roseomonas mucosa	strain=NCTC13291	GCA_900455935.1	207340	207340	type	True	77.2395	300	1152	95	below_threshold
Roseomonas mucosa	strain=ATCC BAA-692	GCA_000622225.1	207340	207340	type	True	77.1123	309	1152	95	below_threshold
Acetobacter garciniae	strain=TBRC 12339	GCA_017377735.1	2817435	2817435	type	True	77.0185	149	1152	95	below_threshold
Rhodovarius crocodyli	strain=CCP-6	GCA_004005855.1	1979269	1979269	type	True	76.8143	256	1152	95	below_threshold
Elioraea tepida	strain=MS-P2	GCA_019203965.1	2843330	2843330	type	True	76.6923	218	1152	95	below_threshold
Rhodoligotrophos defluvii	strain=lm1	GCA_005281615.1	2561934	2561934	type	True	75.7425	135	1152	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:54,202] [INFO] DFAST Taxonomy check result was written to GCF_026341395.1_ASM2634139v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:54,202] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:54,202] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:54,202] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7984919c-3c5a-4952-9ea9-4aff27eb21a6/dqc_reference/checkm_data
[2024-01-24 13:49:54,203] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:54,247] [INFO] Task started: CheckM
[2024-01-24 13:49:54,248] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_026341395.1_ASM2634139v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_026341395.1_ASM2634139v1_genomic.fna/checkm_input GCF_026341395.1_ASM2634139v1_genomic.fna/checkm_result
[2024-01-24 13:50:34,894] [INFO] Task succeeded: CheckM
[2024-01-24 13:50:34,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:50:34,920] [INFO] ===== Completeness check finished =====
[2024-01-24 13:50:34,920] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:50:34,921] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_026341395.1_ASM2634139v1_genomic.fna/markers.fasta)
[2024-01-24 13:50:34,921] [INFO] Task started: Blastn
[2024-01-24 13:50:34,922] [INFO] Running command: blastn -query GCF_026341395.1_ASM2634139v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7984919c-3c5a-4952-9ea9-4aff27eb21a6/dqc_reference/reference_markers_gtdb.fasta -out GCF_026341395.1_ASM2634139v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:37,761] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:37,765] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:37,766] [INFO] Target genome list was writen to GCF_026341395.1_ASM2634139v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:37,779] [INFO] Task started: fastANI
[2024-01-24 13:50:37,779] [INFO] Running command: fastANI --query /var/lib/cwl/stgc2f63626-7060-40bf-b0e5-d604f956a4a0/GCF_026341395.1_ASM2634139v1_genomic.fna.gz --refList GCF_026341395.1_ASM2634139v1_genomic.fna/target_genomes_gtdb.txt --output GCF_026341395.1_ASM2634139v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:52,418] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:52,432] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:52,432] [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_014192375.1	s__Endobacter medicaginis	99.9838	1128	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Endobacter	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCA_903844135.1	s__Lichenicola sp903844135	79.1419	462	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.79	99.79	0.94	0.94	2	-
GCF_005844085.1	s__Lichenicoccus roseus	78.7004	443	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicoccus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013201075.1	s__Lichenicola cladoniae	78.4073	409	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Lichenicola	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000964365.1	s__Acidisphaera rubrifaciens	78.1008	215	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Acidisphaera	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014174375.1	s__Gluconacetobacter asukensis	78.0401	322	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	96.0437	N/A	N/A	N/A	N/A	1	-
GCA_003133265.1	s__PALSA-911 sp003133265	77.9103	237	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__PALSA-911	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021325.1	s__Gluconacetobacter diazotrophicus	77.9018	322	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.14	98.86	0.90	0.85	4	-
GCF_014174355.1	s__Gluconacetobacter azotocaptans	77.7939	313	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Gluconacetobacter	95.0	99.32	99.32	0.91	0.91	2	-
GCA_903907955.1	s__BOG-930 sp903907955	77.7063	311	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.93	99.75	0.97	0.94	12	-
GCF_008630155.1	s__Rhodovastum atsumiense	77.6777	374	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Rhodovastum	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001899585.1	s__70-18 sp001899585	77.6652	387	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__70-18	95.0	99.94	99.94	0.98	0.98	2	-
GCF_000164635.1	s__Roseomonas cervicalis	77.5288	306	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Roseomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002906255.1	s__Komagataeibacter maltaceti	77.5199	208	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Komagataeibacter	95.0	99.99	99.99	0.97	0.97	2	-
GCA_903918195.1	s__BOG-930 sp903918195	77.4453	284	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__BOG-930	95.0	99.84	99.84	0.94	0.94	2	-
GCF_003258945.1	s__Paracraurococcus frigidaeris	77.1854	383	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Paracraurococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004761865.1	s__Crenalkalicoccus roseus	77.0538	331	1152	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Acetobacterales;f__Acetobacteraceae;g__Crenalkalicoccus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:50:52,434] [INFO] GTDB search result was written to GCF_026341395.1_ASM2634139v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:52,434] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:52,439] [INFO] DFAST_QC result json was written to GCF_026341395.1_ASM2634139v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:52,439] [INFO] DFAST_QC completed!
[2024-01-24 13:50:52,439] [INFO] Total running time: 0h1m25s