[2024-01-24 12:46:55,930] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:55,935] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:55,935] [INFO] DQC Reference Directory: /var/lib/cwl/stga0c9cb85-90e9-40c0-b490-e6045e4d2c5c/dqc_reference
[2024-01-24 12:46:57,209] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:57,210] [INFO] Task started: Prodigal
[2024-01-24 12:46:57,210] [INFO] Running command: gunzip -c /var/lib/cwl/stg9196b53e-7558-4b99-bdbd-b4ef9a1bd6e1/GCF_007989765.1_ASM798976v1_genomic.fna.gz | prodigal -d GCF_007989765.1_ASM798976v1_genomic.fna/cds.fna -a GCF_007989765.1_ASM798976v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:01,924] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:01,924] [INFO] Task started: HMMsearch
[2024-01-24 12:47:01,925] [INFO] Running command: hmmsearch --tblout GCF_007989765.1_ASM798976v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga0c9cb85-90e9-40c0-b490-e6045e4d2c5c/dqc_reference/reference_markers.hmm GCF_007989765.1_ASM798976v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:02,161] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:02,162] [INFO] Found 6/6 markers.
[2024-01-24 12:47:02,186] [INFO] Query marker FASTA was written to GCF_007989765.1_ASM798976v1_genomic.fna/markers.fasta
[2024-01-24 12:47:02,187] [INFO] Task started: Blastn
[2024-01-24 12:47:02,187] [INFO] Running command: blastn -query GCF_007989765.1_ASM798976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0c9cb85-90e9-40c0-b490-e6045e4d2c5c/dqc_reference/reference_markers.fasta -out GCF_007989765.1_ASM798976v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:02,768] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:02,771] [INFO] Selected 23 target genomes.
[2024-01-24 12:47:02,772] [INFO] Target genome list was writen to GCF_007989765.1_ASM798976v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:02,805] [INFO] Task started: fastANI
[2024-01-24 12:47:02,805] [INFO] Running command: fastANI --query /var/lib/cwl/stg9196b53e-7558-4b99-bdbd-b4ef9a1bd6e1/GCF_007989765.1_ASM798976v1_genomic.fna.gz --refList GCF_007989765.1_ASM798976v1_genomic.fna/target_genomes.txt --output GCF_007989765.1_ASM798976v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:11,298] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:11,298] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga0c9cb85-90e9-40c0-b490-e6045e4d2c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:11,298] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga0c9cb85-90e9-40c0-b490-e6045e4d2c5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:11,306] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:47:11,306] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:11,306] [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
Furfurilactobacillus siliginis	strain=NBRC 101315	GCA_007989765.1	348151	348151	type	True	100.0	622	626	95	conclusive
Furfurilactobacillus siliginis	strain=DSM 22696	GCA_001437435.1	348151	348151	type	True	99.9878	622	626	95	conclusive
Furfurilactobacillus milii	strain=FUA3430	GCA_021654115.1	2888272	2888272	type	True	80.1869	180	626	95	below_threshold
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_000277855.1	231049	231049	type	True	79.3666	180	626	95	below_threshold
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_001435135.1	231049	231049	type	True	79.2307	179	626	95	below_threshold
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_000428925.1	231049	231049	type	True	79.0906	185	626	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	78.9876	54	626	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:11,307] [INFO] DFAST Taxonomy check result was written to GCF_007989765.1_ASM798976v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:11,308] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:11,308] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:11,308] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga0c9cb85-90e9-40c0-b490-e6045e4d2c5c/dqc_reference/checkm_data
[2024-01-24 12:47:11,309] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:11,331] [INFO] Task started: CheckM
[2024-01-24 12:47:11,331] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007989765.1_ASM798976v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007989765.1_ASM798976v1_genomic.fna/checkm_input GCF_007989765.1_ASM798976v1_genomic.fna/checkm_result
[2024-01-24 12:47:32,775] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:32,776] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:32,792] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:32,792] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:32,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007989765.1_ASM798976v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:32,793] [INFO] Task started: Blastn
[2024-01-24 12:47:32,793] [INFO] Running command: blastn -query GCF_007989765.1_ASM798976v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga0c9cb85-90e9-40c0-b490-e6045e4d2c5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_007989765.1_ASM798976v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:33,603] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:33,608] [INFO] Selected 25 target genomes.
[2024-01-24 12:47:33,608] [INFO] Target genome list was writen to GCF_007989765.1_ASM798976v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:33,629] [INFO] Task started: fastANI
[2024-01-24 12:47:33,630] [INFO] Running command: fastANI --query /var/lib/cwl/stg9196b53e-7558-4b99-bdbd-b4ef9a1bd6e1/GCF_007989765.1_ASM798976v1_genomic.fna.gz --refList GCF_007989765.1_ASM798976v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007989765.1_ASM798976v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:44,348] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:44,356] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:44,356] [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_001437435.1	s__Furfurilactobacillus siliginis	99.9878	622	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_003946345.1	s__Levilactobacillus tongjiangensis	80.4305	52	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013394045.1	s__Furfurilactobacillus rossiae_A	80.0563	193	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	97.68	95.37	0.95	0.90	3	-
GCF_009864005.1	s__Furfurilactobacillus rossiae_B	79.5839	188	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428925.1	s__Furfurilactobacillus rossiae	79.0803	186	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.59	97.96	0.97	0.87	6	-
GCF_003946245.1	s__Levilactobacillus cerevisiae	78.9876	54	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003482405.1	s__Furfurilactobacillus sp003482405	78.905	136	626	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.38	99.38	0.79	0.79	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:44,358] [INFO] GTDB search result was written to GCF_007989765.1_ASM798976v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:44,358] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:44,360] [INFO] DFAST_QC result json was written to GCF_007989765.1_ASM798976v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:44,361] [INFO] DFAST_QC completed!
[2024-01-24 12:47:44,361] [INFO] Total running time: 0h0m48s