[2024-01-24 13:46:43,689] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:43,691] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:43,691] [INFO] DQC Reference Directory: /var/lib/cwl/stg66bede94-b945-4edf-b8d7-dc321416477f/dqc_reference
[2024-01-24 13:46:44,988] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:44,989] [INFO] Task started: Prodigal
[2024-01-24 13:46:44,989] [INFO] Running command: gunzip -c /var/lib/cwl/stg77ff870d-5356-4f49-884d-435760bdb72d/GCF_021654115.1_ASM2165411v1_genomic.fna.gz | prodigal -d GCF_021654115.1_ASM2165411v1_genomic.fna/cds.fna -a GCF_021654115.1_ASM2165411v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:51,829] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:51,830] [INFO] Task started: HMMsearch
[2024-01-24 13:46:51,830] [INFO] Running command: hmmsearch --tblout GCF_021654115.1_ASM2165411v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg66bede94-b945-4edf-b8d7-dc321416477f/dqc_reference/reference_markers.hmm GCF_021654115.1_ASM2165411v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:52,089] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:52,091] [INFO] Found 6/6 markers.
[2024-01-24 13:46:52,120] [INFO] Query marker FASTA was written to GCF_021654115.1_ASM2165411v1_genomic.fna/markers.fasta
[2024-01-24 13:46:52,120] [INFO] Task started: Blastn
[2024-01-24 13:46:52,121] [INFO] Running command: blastn -query GCF_021654115.1_ASM2165411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66bede94-b945-4edf-b8d7-dc321416477f/dqc_reference/reference_markers.fasta -out GCF_021654115.1_ASM2165411v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:52,722] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:52,727] [INFO] Selected 13 target genomes.
[2024-01-24 13:46:52,727] [INFO] Target genome list was writen to GCF_021654115.1_ASM2165411v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:52,741] [INFO] Task started: fastANI
[2024-01-24 13:46:52,741] [INFO] Running command: fastANI --query /var/lib/cwl/stg77ff870d-5356-4f49-884d-435760bdb72d/GCF_021654115.1_ASM2165411v1_genomic.fna.gz --refList GCF_021654115.1_ASM2165411v1_genomic.fna/target_genomes.txt --output GCF_021654115.1_ASM2165411v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:58,768] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:58,769] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg66bede94-b945-4edf-b8d7-dc321416477f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:58,769] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg66bede94-b945-4edf-b8d7-dc321416477f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:58,777] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:58,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:58,777] [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 milii	strain=FUA3430	GCA_021654115.1	2888272	2888272	type	True	100.0	871	871	95	conclusive
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_000277855.1	231049	231049	type	True	93.0821	764	871	95	below_threshold
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_000428925.1	231049	231049	type	True	93.0443	770	871	95	below_threshold
Furfurilactobacillus rossiae	strain=DSM 15814	GCA_001435135.1	231049	231049	type	True	93.0421	763	871	95	below_threshold
Furfurilactobacillus siliginis	strain=DSM 22696	GCA_001437435.1	348151	348151	type	True	79.9212	188	871	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	79.0977	51	871	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:58,779] [INFO] DFAST Taxonomy check result was written to GCF_021654115.1_ASM2165411v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:58,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:58,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:58,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg66bede94-b945-4edf-b8d7-dc321416477f/dqc_reference/checkm_data
[2024-01-24 13:46:58,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:58,814] [INFO] Task started: CheckM
[2024-01-24 13:46:58,815] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_021654115.1_ASM2165411v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_021654115.1_ASM2165411v1_genomic.fna/checkm_input GCF_021654115.1_ASM2165411v1_genomic.fna/checkm_result
[2024-01-24 13:47:25,359] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:25,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:25,378] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:25,378] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:25,378] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_021654115.1_ASM2165411v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:25,379] [INFO] Task started: Blastn
[2024-01-24 13:47:25,379] [INFO] Running command: blastn -query GCF_021654115.1_ASM2165411v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg66bede94-b945-4edf-b8d7-dc321416477f/dqc_reference/reference_markers_gtdb.fasta -out GCF_021654115.1_ASM2165411v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:26,170] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:26,173] [INFO] Selected 12 target genomes.
[2024-01-24 13:47:26,173] [INFO] Target genome list was writen to GCF_021654115.1_ASM2165411v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:26,191] [INFO] Task started: fastANI
[2024-01-24 13:47:26,192] [INFO] Running command: fastANI --query /var/lib/cwl/stg77ff870d-5356-4f49-884d-435760bdb72d/GCF_021654115.1_ASM2165411v1_genomic.fna.gz --refList GCF_021654115.1_ASM2165411v1_genomic.fna/target_genomes_gtdb.txt --output GCF_021654115.1_ASM2165411v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:31,712] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:31,720] [INFO] Found 5 fastANI hits (2 hits with ANI > circumscription radius)
[2024-01-24 13:47:31,720] [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_013394045.1	s__Furfurilactobacillus rossiae_A	98.6774	811	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	97.68	95.37	0.95	0.90	3	inconclusive
GCF_009864005.1	s__Furfurilactobacillus rossiae_B	95.042	757	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	N/A	N/A	N/A	N/A	1	inconclusive
GCF_000428925.1	s__Furfurilactobacillus rossiae	93.0295	771	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.59	97.96	0.97	0.87	6	-
GCA_003482405.1	s__Furfurilactobacillus sp003482405	80.4807	313	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.38	99.38	0.79	0.79	2	-
GCF_001437435.1	s__Furfurilactobacillus siliginis	79.9212	188	871	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Furfurilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:31,722] [INFO] GTDB search result was written to GCF_021654115.1_ASM2165411v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:31,722] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:31,725] [INFO] DFAST_QC result json was written to GCF_021654115.1_ASM2165411v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:31,725] [INFO] DFAST_QC completed!
[2024-01-24 13:47:31,725] [INFO] Total running time: 0h0m48s