[2024-01-24 12:31:21,171] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,173] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,173] [INFO] DQC Reference Directory: /var/lib/cwl/stgef05f10b-2b05-4f64-b6bc-1f8de8d976c2/dqc_reference
[2024-01-24 12:31:22,450] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,450] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,451] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f09ea6f-b4af-4e51-a4cf-1178b325d52f/GCF_002762335.1_ASM276233v1_genomic.fna.gz | prodigal -d GCF_002762335.1_ASM276233v1_genomic.fna/cds.fna -a GCF_002762335.1_ASM276233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:25,587] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:25,588] [INFO] Task started: HMMsearch
[2024-01-24 12:31:25,588] [INFO] Running command: hmmsearch --tblout GCF_002762335.1_ASM276233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgef05f10b-2b05-4f64-b6bc-1f8de8d976c2/dqc_reference/reference_markers.hmm GCF_002762335.1_ASM276233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:25,751] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:25,752] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg7f09ea6f-b4af-4e51-a4cf-1178b325d52f/GCF_002762335.1_ASM276233v1_genomic.fna.gz]
[2024-01-24 12:31:25,770] [INFO] Query marker FASTA was written to GCF_002762335.1_ASM276233v1_genomic.fna/markers.fasta
[2024-01-24 12:31:25,770] [INFO] Task started: Blastn
[2024-01-24 12:31:25,771] [INFO] Running command: blastn -query GCF_002762335.1_ASM276233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef05f10b-2b05-4f64-b6bc-1f8de8d976c2/dqc_reference/reference_markers.fasta -out GCF_002762335.1_ASM276233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:26,419] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:26,422] [INFO] Selected 22 target genomes.
[2024-01-24 12:31:26,422] [INFO] Target genome list was writen to GCF_002762335.1_ASM276233v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:26,431] [INFO] Task started: fastANI
[2024-01-24 12:31:26,431] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f09ea6f-b4af-4e51-a4cf-1178b325d52f/GCF_002762335.1_ASM276233v1_genomic.fna.gz --refList GCF_002762335.1_ASM276233v1_genomic.fna/target_genomes.txt --output GCF_002762335.1_ASM276233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:34,280] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:34,280] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgef05f10b-2b05-4f64-b6bc-1f8de8d976c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:34,280] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgef05f10b-2b05-4f64-b6bc-1f8de8d976c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:34,295] [INFO] Found 19 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:31:34,295] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:31:34,295] [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
Companilactobacillus bobalius	strain=203	GCA_009764355.1	2801451	2801451	type	True	78.811	104	516	95	below_threshold
Companilactobacillus kedongensis	strain=116-2	GCA_003946625.1	2486004	2486004	type	True	78.7421	106	516	95	below_threshold
Companilactobacillus crustorum	strain=LMG 23699	GCA_001438825.1	392416	392416	type	True	78.4725	101	516	95	below_threshold
Companilactobacillus suantsaicola	strain=BCRC 81127	GCA_004745525.1	2487723	2487723	type	True	78.4284	90	516	95	below_threshold
Companilactobacillus bobalius	strain=DSM 19674	GCA_001434855.1	2801451	2801451	type	True	78.4079	101	516	95	below_threshold
Companilactobacillus tucceti	strain=DSM 20183	GCA_001434665.1	238012	238012	type	True	78.3592	125	516	95	below_threshold
Companilactobacillus crustorum	strain=JCM 15951	GCA_001434585.1	392416	392416	type	True	78.3054	102	516	95	below_threshold
Companilactobacillus ginsenosidimutans	strain=EMML 3041	GCA_001050475.1	1007676	1007676	type	True	78.2928	130	516	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_009764365.1	2801452	2801452	type	True	78.2883	121	516	95	below_threshold
Companilactobacillus paralimentarius	strain=DSM 13238	GCA_009764345.1	83526	83526	type	True	78.2561	108	516	95	below_threshold
Companilactobacillus mishanensis	strain=256-3	GCA_003946505.1	2486008	2486008	type	True	78.2392	117	516	95	below_threshold
Companilactobacillus nuruki	strain=SYF10-1a	GCA_002872255.1	1993540	1993540	type	True	78.176	120	516	95	below_threshold
Companilactobacillus hulinensis	strain=8-1(1)	GCA_003946555.1	2486007	2486007	type	True	78.1659	121	516	95	below_threshold
Companilactobacillus kimchii	strain=JCM 10707	GCA_001311095.1	2801452	2801452	type	True	78.1128	115	516	95	below_threshold
Companilactobacillus halodurans	strain=TMW 1.2172	GCA_009600985.1	2584183	2584183	type	True	78.1123	96	516	95	below_threshold
Companilactobacillus mindensis	strain=DSM 14500	GCA_001434275.1	167481	167481	type	True	78.075	92	516	95	below_threshold
Companilactobacillus huachuanensis	strain=395-6.2	GCA_005404815.1	2559914	2559914	type	True	78.0368	110	516	95	below_threshold
Companilactobacillus kimchii	strain=DSM 13961	GCA_001435445.1	2801452	2801452	type	True	78.0126	118	516	95	below_threshold
Companilactobacillus futsaii	strain=JCM 17355	GCA_001435505.1	938155	938155	type	True	77.7594	116	516	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:34,297] [INFO] DFAST Taxonomy check result was written to GCF_002762335.1_ASM276233v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:34,298] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:34,298] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:34,299] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgef05f10b-2b05-4f64-b6bc-1f8de8d976c2/dqc_reference/checkm_data
[2024-01-24 12:31:34,300] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:34,316] [INFO] Task started: CheckM
[2024-01-24 12:31:34,317] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002762335.1_ASM276233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002762335.1_ASM276233v1_genomic.fna/checkm_input GCF_002762335.1_ASM276233v1_genomic.fna/checkm_result
[2024-01-24 12:31:50,518] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:50,519] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:50,538] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:50,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:50,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002762335.1_ASM276233v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:50,539] [INFO] Task started: Blastn
[2024-01-24 12:31:50,539] [INFO] Running command: blastn -query GCF_002762335.1_ASM276233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgef05f10b-2b05-4f64-b6bc-1f8de8d976c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_002762335.1_ASM276233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:51,336] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:51,341] [INFO] Selected 15 target genomes.
[2024-01-24 12:31:51,341] [INFO] Target genome list was writen to GCF_002762335.1_ASM276233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:51,350] [INFO] Task started: fastANI
[2024-01-24 12:31:51,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f09ea6f-b4af-4e51-a4cf-1178b325d52f/GCF_002762335.1_ASM276233v1_genomic.fna.gz --refList GCF_002762335.1_ASM276233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002762335.1_ASM276233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:57,213] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:57,225] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:57,226] [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_004117915.1	s__Companilactobacillus metriopterae	97.3931	454	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	97.46	97.46	0.91	0.91	2	conclusive
GCF_009764355.1	s__Companilactobacillus paralimentarius_A	78.9659	105	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.92	99.92	1.00	0.99	4	-
GCF_003946625.1	s__Companilactobacillus kedongensis	78.7421	106	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745525.1	s__Companilactobacillus suantsaicola	78.4732	89	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001050475.1	s__Companilactobacillus ginsenosidimutans	78.463	132	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434665.1	s__Companilactobacillus tucceti	78.3592	125	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434585.1	s__Companilactobacillus crustorum	78.3054	102	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.76	99.52	0.96	0.87	5	-
GCF_003946015.1	s__Companilactobacillus insicii	78.2671	126	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946505.1	s__Companilactobacillus mishanensis	78.2392	117	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	98.34	97.53	0.96	0.93	4	-
GCF_002872255.1	s__Companilactobacillus nuruki	78.2043	119	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946555.1	s__Companilactobacillus hulinensis	78.1659	121	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434275.1	s__Companilactobacillus mindensis	78.075	92	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001435445.1	s__Companilactobacillus kimchii	78.0745	119	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.99	99.97	1.00	1.00	5	-
GCF_001435505.1	s__Companilactobacillus futsaii	77.7594	116	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	99.20	98.55	0.91	0.87	7	-
GCA_019116025.1	s__Companilactobacillus pullicola	77.0342	94	516	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Companilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:57,227] [INFO] GTDB search result was written to GCF_002762335.1_ASM276233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:57,228] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:57,232] [INFO] DFAST_QC result json was written to GCF_002762335.1_ASM276233v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:57,233] [INFO] DFAST_QC completed!
[2024-01-24 12:31:57,233] [INFO] Total running time: 0h0m36s