[2024-01-24 13:12:39,048] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:12:39,050] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:12:39,050] [INFO] DQC Reference Directory: /var/lib/cwl/stgc39d32ee-b3b6-4879-8368-fffc9f073cf4/dqc_reference
[2024-01-24 13:12:40,369] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:12:40,370] [INFO] Task started: Prodigal
[2024-01-24 13:12:40,370] [INFO] Running command: gunzip -c /var/lib/cwl/stgc86aa6d7-9265-4248-82e0-5b5279525232/GCF_001047135.2_ASM104713v2_genomic.fna.gz | prodigal -d GCF_001047135.2_ASM104713v2_genomic.fna/cds.fna -a GCF_001047135.2_ASM104713v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:12:44,807] [INFO] Task succeeded: Prodigal
[2024-01-24 13:12:44,807] [INFO] Task started: HMMsearch
[2024-01-24 13:12:44,807] [INFO] Running command: hmmsearch --tblout GCF_001047135.2_ASM104713v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc39d32ee-b3b6-4879-8368-fffc9f073cf4/dqc_reference/reference_markers.hmm GCF_001047135.2_ASM104713v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:12:45,051] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:12:45,052] [INFO] Found 6/6 markers.
[2024-01-24 13:12:45,076] [INFO] Query marker FASTA was written to GCF_001047135.2_ASM104713v2_genomic.fna/markers.fasta
[2024-01-24 13:12:45,076] [INFO] Task started: Blastn
[2024-01-24 13:12:45,076] [INFO] Running command: blastn -query GCF_001047135.2_ASM104713v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc39d32ee-b3b6-4879-8368-fffc9f073cf4/dqc_reference/reference_markers.fasta -out GCF_001047135.2_ASM104713v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:12:45,757] [INFO] Task succeeded: Blastn
[2024-01-24 13:12:45,761] [INFO] Selected 17 target genomes.
[2024-01-24 13:12:45,761] [INFO] Target genome list was writen to GCF_001047135.2_ASM104713v2_genomic.fna/target_genomes.txt
[2024-01-24 13:12:45,802] [INFO] Task started: fastANI
[2024-01-24 13:12:45,802] [INFO] Running command: fastANI --query /var/lib/cwl/stgc86aa6d7-9265-4248-82e0-5b5279525232/GCF_001047135.2_ASM104713v2_genomic.fna.gz --refList GCF_001047135.2_ASM104713v2_genomic.fna/target_genomes.txt --output GCF_001047135.2_ASM104713v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:12:50,964] [INFO] Task succeeded: fastANI
[2024-01-24 13:12:50,964] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc39d32ee-b3b6-4879-8368-fffc9f073cf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:12:50,964] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc39d32ee-b3b6-4879-8368-fffc9f073cf4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:12:50,978] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:12:50,978] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:12:50,979] [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
Fructobacillus tropaeoli	strain=F214-1	GCA_001047135.2	709323	709323	type	True	100.0	526	527	95	conclusive
Fructobacillus pseudoficulneus	strain=DSM 15468	GCA_001047115.2	220714	220714	type	True	82.4061	257	527	95	below_threshold
Fructobacillus pseudoficulneus	strain=DSM 15468	GCA_900108455.1	220714	220714	type	True	82.2327	253	527	95	below_threshold
Fructobacillus ficulneus	strain=JCM 12225	GCA_001047075.2	157463	157463	type	True	81.048	225	527	95	below_threshold
Fructobacillus durionis	strain=DSM 19113	GCA_900112405.1	283737	283737	type	True	79.8818	140	527	95	below_threshold
Fructobacillus broussonetiae	strain=M2-14	GCA_018437275.1	2713173	2713173	type	True	79.7631	128	527	95	below_threshold
Fructobacillus parabroussonetiae	strain=S1-1	GCA_018437265.1	2713174	2713174	type	True	79.6865	130	527	95	below_threshold
Fructobacillus papyrifericola	strain=M1-21	GCA_018437235.1	2713172	2713172	type	True	79.6226	154	527	95	below_threshold
Leuconostoc pseudomesenteroides	strain=FDAARGOS_1003	GCA_016127255.1	33968	33968	suspected-type	True	78.9917	51	527	95	below_threshold
Leuconostoc pseudomesenteroides	strain=NCDO 768	GCA_012396745.1	33968	33968	suspected-type	True	78.8467	52	527	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:12:50,989] [INFO] DFAST Taxonomy check result was written to GCF_001047135.2_ASM104713v2_genomic.fna/tc_result.tsv
[2024-01-24 13:12:50,990] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:12:50,990] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:12:50,991] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc39d32ee-b3b6-4879-8368-fffc9f073cf4/dqc_reference/checkm_data
[2024-01-24 13:12:50,992] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:12:51,011] [INFO] Task started: CheckM
[2024-01-24 13:12:51,011] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001047135.2_ASM104713v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001047135.2_ASM104713v2_genomic.fna/checkm_input GCF_001047135.2_ASM104713v2_genomic.fna/checkm_result
[2024-01-24 13:13:11,698] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:11,699] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:11,716] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:11,717] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:11,717] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001047135.2_ASM104713v2_genomic.fna/markers.fasta)
[2024-01-24 13:13:11,718] [INFO] Task started: Blastn
[2024-01-24 13:13:11,718] [INFO] Running command: blastn -query GCF_001047135.2_ASM104713v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc39d32ee-b3b6-4879-8368-fffc9f073cf4/dqc_reference/reference_markers_gtdb.fasta -out GCF_001047135.2_ASM104713v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:12,497] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:12,500] [INFO] Selected 11 target genomes.
[2024-01-24 13:13:12,501] [INFO] Target genome list was writen to GCF_001047135.2_ASM104713v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:12,539] [INFO] Task started: fastANI
[2024-01-24 13:13:12,539] [INFO] Running command: fastANI --query /var/lib/cwl/stgc86aa6d7-9265-4248-82e0-5b5279525232/GCF_001047135.2_ASM104713v2_genomic.fna.gz --refList GCF_001047135.2_ASM104713v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001047135.2_ASM104713v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:16,038] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:16,045] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:16,046] [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_001047135.2	s__Fructobacillus tropaeoli	100.0	526	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	97.33	96.88	0.89	0.88	3	conclusive
GCF_001038455.1	s__Fructobacillus sp001038455	94.7122	433	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108455.1	s__Fructobacillus pseudoficulneus	82.2171	253	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001047075.2	s__Fructobacillus ficulneus	81.0206	226	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112405.1	s__Fructobacillus durionis	79.8918	139	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018437275.1	s__Fructobacillus sp018437275	79.7631	128	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018437235.1	s__Fructobacillus sp018437235	79.6226	154	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014634745.1	s__Leuconostoc pseudomesenteroides	78.9189	50	527	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	97.98	96.85	0.90	0.84	11	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:16,047] [INFO] GTDB search result was written to GCF_001047135.2_ASM104713v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:16,048] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:16,051] [INFO] DFAST_QC result json was written to GCF_001047135.2_ASM104713v2_genomic.fna/dqc_result.json
[2024-01-24 13:13:16,051] [INFO] DFAST_QC completed!
[2024-01-24 13:13:16,051] [INFO] Total running time: 0h0m37s