[2024-01-24 13:49:19,205] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:19,208] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:19,209] [INFO] DQC Reference Directory: /var/lib/cwl/stg08a1a16c-b68d-4e83-8281-f9ba5ddfb918/dqc_reference
[2024-01-24 13:49:20,756] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:20,758] [INFO] Task started: Prodigal
[2024-01-24 13:49:20,758] [INFO] Running command: gunzip -c /var/lib/cwl/stgdd6f8e9b-8045-41e8-8275-6c676b1ec2b4/GCF_001047075.2_ASM104707v2_genomic.fna.gz | prodigal -d GCF_001047075.2_ASM104707v2_genomic.fna/cds.fna -a GCF_001047075.2_ASM104707v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:24,717] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:24,718] [INFO] Task started: HMMsearch
[2024-01-24 13:49:24,718] [INFO] Running command: hmmsearch --tblout GCF_001047075.2_ASM104707v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08a1a16c-b68d-4e83-8281-f9ba5ddfb918/dqc_reference/reference_markers.hmm GCF_001047075.2_ASM104707v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:24,940] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:24,942] [INFO] Found 6/6 markers.
[2024-01-24 13:49:24,969] [INFO] Query marker FASTA was written to GCF_001047075.2_ASM104707v2_genomic.fna/markers.fasta
[2024-01-24 13:49:24,969] [INFO] Task started: Blastn
[2024-01-24 13:49:24,969] [INFO] Running command: blastn -query GCF_001047075.2_ASM104707v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg08a1a16c-b68d-4e83-8281-f9ba5ddfb918/dqc_reference/reference_markers.fasta -out GCF_001047075.2_ASM104707v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:25,606] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:25,609] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:25,609] [INFO] Target genome list was writen to GCF_001047075.2_ASM104707v2_genomic.fna/target_genomes.txt
[2024-01-24 13:49:25,618] [INFO] Task started: fastANI
[2024-01-24 13:49:25,618] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd6f8e9b-8045-41e8-8275-6c676b1ec2b4/GCF_001047075.2_ASM104707v2_genomic.fna.gz --refList GCF_001047075.2_ASM104707v2_genomic.fna/target_genomes.txt --output GCF_001047075.2_ASM104707v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:30,696] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:30,697] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08a1a16c-b68d-4e83-8281-f9ba5ddfb918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:30,697] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08a1a16c-b68d-4e83-8281-f9ba5ddfb918/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:30,707] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:30,707] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:30,707] [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 ficulneus	strain=JCM 12225	GCA_001047075.2	157463	157463	type	True	99.9999	505	507	95	conclusive
Fructobacillus tropaeoli	strain=F214-1	GCA_001047135.2	709323	709323	type	True	81.0058	230	507	95	below_threshold
Fructobacillus pseudoficulneus	strain=DSM 15468	GCA_001047115.2	220714	220714	type	True	80.7203	244	507	95	below_threshold
Fructobacillus pseudoficulneus	strain=DSM 15468	GCA_900108455.1	220714	220714	type	True	80.5866	241	507	95	below_threshold
Fructobacillus durionis	strain=DSM 19113	GCA_900112405.1	283737	283737	type	True	79.9785	137	507	95	below_threshold
Fructobacillus broussonetiae	strain=M2-14	GCA_018437275.1	2713173	2713173	type	True	79.8954	123	507	95	below_threshold
Fructobacillus papyrifericola	strain=M1-21	GCA_018437235.1	2713172	2713172	type	True	79.5553	120	507	95	below_threshold
Fructobacillus parabroussonetiae	strain=S1-1	GCA_018437265.1	2713174	2713174	type	True	79.5254	116	507	95	below_threshold
Fructobacillus papyriferae	strain=M1-10	GCA_018437225.1	2713171	2713171	type	True	79.4435	101	507	95	below_threshold
Fructobacillus fructosus	strain=NRIC 1058	GCA_001047095.2	1631	1631	type	True	79.3655	114	507	95	below_threshold
Fructobacillus fructosus	strain=KCTC 3544	GCA_000185045.2	1631	1631	type	True	79.364	119	507	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:30,709] [INFO] DFAST Taxonomy check result was written to GCF_001047075.2_ASM104707v2_genomic.fna/tc_result.tsv
[2024-01-24 13:49:30,709] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:30,710] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:30,710] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08a1a16c-b68d-4e83-8281-f9ba5ddfb918/dqc_reference/checkm_data
[2024-01-24 13:49:30,711] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:30,731] [INFO] Task started: CheckM
[2024-01-24 13:49:30,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001047075.2_ASM104707v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001047075.2_ASM104707v2_genomic.fna/checkm_input GCF_001047075.2_ASM104707v2_genomic.fna/checkm_result
[2024-01-24 13:49:50,696] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:50,698] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:50,724] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:50,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:50,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001047075.2_ASM104707v2_genomic.fna/markers.fasta)
[2024-01-24 13:49:50,726] [INFO] Task started: Blastn
[2024-01-24 13:49:50,726] [INFO] Running command: blastn -query GCF_001047075.2_ASM104707v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg08a1a16c-b68d-4e83-8281-f9ba5ddfb918/dqc_reference/reference_markers_gtdb.fasta -out GCF_001047075.2_ASM104707v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:51,676] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:51,682] [INFO] Selected 16 target genomes.
[2024-01-24 13:49:51,682] [INFO] Target genome list was writen to GCF_001047075.2_ASM104707v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:51,692] [INFO] Task started: fastANI
[2024-01-24 13:49:51,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgdd6f8e9b-8045-41e8-8275-6c676b1ec2b4/GCF_001047075.2_ASM104707v2_genomic.fna.gz --refList GCF_001047075.2_ASM104707v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001047075.2_ASM104707v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:56,620] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:56,629] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:56,630] [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_001047075.2	s__Fructobacillus ficulneus	99.9999	505	507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001047135.2	s__Fructobacillus tropaeoli	81.0058	230	507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	97.33	96.88	0.89	0.88	3	-
GCF_001038455.1	s__Fructobacillus sp001038455	81.0019	218	507	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	80.5613	242	507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_900112405.1	s__Fructobacillus durionis	79.9785	137	507	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	79.5553	120	507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018437265.1	s__Fructobacillus sp018437265	79.5254	116	507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018437225.1	s__Fructobacillus sp018437225	79.4435	101	507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001438695.1	s__Fructobacillus fructosus	79.2226	122	507	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.37	98.18	0.96	0.91	4	-
--------------------------------------------------------------------------------
[2024-01-24 13:49:56,631] [INFO] GTDB search result was written to GCF_001047075.2_ASM104707v2_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:56,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:56,635] [INFO] DFAST_QC result json was written to GCF_001047075.2_ASM104707v2_genomic.fna/dqc_result.json
[2024-01-24 13:49:56,635] [INFO] DFAST_QC completed!
[2024-01-24 13:49:56,635] [INFO] Total running time: 0h0m37s