[2024-01-25 19:45:05,372] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:45:05,374] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:45:05,374] [INFO] DQC Reference Directory: /var/lib/cwl/stg7688e401-588c-4580-ad10-4c43e10777e3/dqc_reference
[2024-01-25 19:45:06,497] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:45:06,498] [INFO] Task started: Prodigal
[2024-01-25 19:45:06,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg4947e3d3-a96b-4c75-9824-4cf46b2d06a3/GCF_024029775.1_ASM2402977v1_genomic.fna.gz | prodigal -d GCF_024029775.1_ASM2402977v1_genomic.fna/cds.fna -a GCF_024029775.1_ASM2402977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:45:09,678] [INFO] Task succeeded: Prodigal
[2024-01-25 19:45:09,678] [INFO] Task started: HMMsearch
[2024-01-25 19:45:09,678] [INFO] Running command: hmmsearch --tblout GCF_024029775.1_ASM2402977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7688e401-588c-4580-ad10-4c43e10777e3/dqc_reference/reference_markers.hmm GCF_024029775.1_ASM2402977v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:45:09,891] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:45:09,892] [INFO] Found 6/6 markers.
[2024-01-25 19:45:09,908] [INFO] Query marker FASTA was written to GCF_024029775.1_ASM2402977v1_genomic.fna/markers.fasta
[2024-01-25 19:45:09,909] [INFO] Task started: Blastn
[2024-01-25 19:45:09,909] [INFO] Running command: blastn -query GCF_024029775.1_ASM2402977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7688e401-588c-4580-ad10-4c43e10777e3/dqc_reference/reference_markers.fasta -out GCF_024029775.1_ASM2402977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:10,459] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:10,462] [INFO] Selected 19 target genomes.
[2024-01-25 19:45:10,462] [INFO] Target genome list was writen to GCF_024029775.1_ASM2402977v1_genomic.fna/target_genomes.txt
[2024-01-25 19:45:10,505] [INFO] Task started: fastANI
[2024-01-25 19:45:10,505] [INFO] Running command: fastANI --query /var/lib/cwl/stg4947e3d3-a96b-4c75-9824-4cf46b2d06a3/GCF_024029775.1_ASM2402977v1_genomic.fna.gz --refList GCF_024029775.1_ASM2402977v1_genomic.fna/target_genomes.txt --output GCF_024029775.1_ASM2402977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:45:15,947] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:15,947] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7688e401-588c-4580-ad10-4c43e10777e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:45:15,948] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7688e401-588c-4580-ad10-4c43e10777e3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:45:15,955] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:45:15,956] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:45:15,956] [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	89.3952	393	471	95	below_threshold
Fructobacillus pseudoficulneus	strain=DSM 15468	GCA_900108455.1	220714	220714	type	True	81.5436	237	471	95	below_threshold
Fructobacillus pseudoficulneus	strain=DSM 15468	GCA_001047115.2	220714	220714	type	True	81.418	237	471	95	below_threshold
Fructobacillus ficulneus	strain=JCM 12225	GCA_001047075.2	157463	157463	type	True	80.6119	194	471	95	below_threshold
Fructobacillus durionis	strain=DSM 19113	GCA_900112405.1	283737	283737	type	True	79.7957	118	471	95	below_threshold
Fructobacillus fructosus	strain=DSM 20349	GCA_001438695.1	1631	1631	type	True	79.727	117	471	95	below_threshold
Fructobacillus fructosus	strain=KCTC 3544	GCA_000185045.2	1631	1631	type	True	79.726	119	471	95	below_threshold
Fructobacillus fructosus	strain=NRIC 1058	GCA_001047095.2	1631	1631	type	True	79.668	118	471	95	below_threshold
Fructobacillus broussonetiae	strain=M2-14	GCA_018437275.1	2713173	2713173	type	True	79.5271	112	471	95	below_threshold
Fructobacillus papyriferae	strain=M1-10	GCA_018437225.1	2713171	2713171	type	True	79.006	113	471	95	below_threshold
Convivina intestini	strain=DSM 28795	GCA_003096575.1	1505726	1505726	type	True	78.9515	87	471	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:45:15,972] [INFO] DFAST Taxonomy check result was written to GCF_024029775.1_ASM2402977v1_genomic.fna/tc_result.tsv
[2024-01-25 19:45:15,973] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:45:15,973] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:45:15,973] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7688e401-588c-4580-ad10-4c43e10777e3/dqc_reference/checkm_data
[2024-01-25 19:45:15,974] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:45:15,990] [INFO] Task started: CheckM
[2024-01-25 19:45:15,990] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024029775.1_ASM2402977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024029775.1_ASM2402977v1_genomic.fna/checkm_input GCF_024029775.1_ASM2402977v1_genomic.fna/checkm_result
[2024-01-25 19:45:31,706] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:31,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:31,721] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:31,721] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:31,721] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024029775.1_ASM2402977v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:31,722] [INFO] Task started: Blastn
[2024-01-25 19:45:31,722] [INFO] Running command: blastn -query GCF_024029775.1_ASM2402977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7688e401-588c-4580-ad10-4c43e10777e3/dqc_reference/reference_markers_gtdb.fasta -out GCF_024029775.1_ASM2402977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:32,476] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:32,479] [INFO] Selected 16 target genomes.
[2024-01-25 19:45:32,479] [INFO] Target genome list was writen to GCF_024029775.1_ASM2402977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:32,490] [INFO] Task started: fastANI
[2024-01-25 19:45:32,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg4947e3d3-a96b-4c75-9824-4cf46b2d06a3/GCF_024029775.1_ASM2402977v1_genomic.fna.gz --refList GCF_024029775.1_ASM2402977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024029775.1_ASM2402977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:45:37,762] [INFO] Task succeeded: fastANI
[2024-01-25 19:45:37,769] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:45:37,769] [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	89.3952	393	471	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	88.9568	391	471	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	81.5889	236	471	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	80.6119	194	471	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	79.8209	117	471	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	79.706	117	471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.37	98.18	0.96	0.91	4	-
GCF_018437275.1	s__Fructobacillus sp018437275	79.5369	111	471	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	79.006	113	471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003096575.1	s__Convivina intestini	78.9761	86	471	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Convivina	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:45:37,771] [INFO] GTDB search result was written to GCF_024029775.1_ASM2402977v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:45:37,771] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:45:37,785] [INFO] DFAST_QC result json was written to GCF_024029775.1_ASM2402977v1_genomic.fna/dqc_result.json
[2024-01-25 19:45:37,785] [INFO] DFAST_QC completed!
[2024-01-25 19:45:37,785] [INFO] Total running time: 0h0m32s