[2024-01-24 13:01:24,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:24,196] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:24,197] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0a0a77d-de3b-4b33-8231-167a0210bb91/dqc_reference
[2024-01-24 13:01:25,581] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:25,582] [INFO] Task started: Prodigal
[2024-01-24 13:01:25,582] [INFO] Running command: gunzip -c /var/lib/cwl/stg0d8a115c-4e4c-4082-9e00-2aabf131fb12/GCF_000185045.1_ASM18504v1_genomic.fna.gz | prodigal -d GCF_000185045.1_ASM18504v1_genomic.fna/cds.fna -a GCF_000185045.1_ASM18504v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:29,452] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:29,453] [INFO] Task started: HMMsearch
[2024-01-24 13:01:29,453] [INFO] Running command: hmmsearch --tblout GCF_000185045.1_ASM18504v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0a0a77d-de3b-4b33-8231-167a0210bb91/dqc_reference/reference_markers.hmm GCF_000185045.1_ASM18504v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:29,691] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:29,693] [INFO] Found 6/6 markers.
[2024-01-24 13:01:29,712] [INFO] Query marker FASTA was written to GCF_000185045.1_ASM18504v1_genomic.fna/markers.fasta
[2024-01-24 13:01:29,712] [INFO] Task started: Blastn
[2024-01-24 13:01:29,713] [INFO] Running command: blastn -query GCF_000185045.1_ASM18504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0a0a77d-de3b-4b33-8231-167a0210bb91/dqc_reference/reference_markers.fasta -out GCF_000185045.1_ASM18504v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:30,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:30,303] [INFO] Selected 9 target genomes.
[2024-01-24 13:01:30,304] [INFO] Target genome list was writen to GCF_000185045.1_ASM18504v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:30,308] [INFO] Task started: fastANI
[2024-01-24 13:01:30,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d8a115c-4e4c-4082-9e00-2aabf131fb12/GCF_000185045.1_ASM18504v1_genomic.fna.gz --refList GCF_000185045.1_ASM18504v1_genomic.fna/target_genomes.txt --output GCF_000185045.1_ASM18504v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:33,237] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:33,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0a0a77d-de3b-4b33-8231-167a0210bb91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:33,238] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0a0a77d-de3b-4b33-8231-167a0210bb91/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:33,248] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 13:01:33,248] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:33,248] [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 fructosus	strain=KCTC 3544	GCA_000185045.2	1631	1631	type	True	100.0	467	468	95	conclusive
Fructobacillus fructosus	strain=DSM 20349	GCA_001438695.1	1631	1631	type	True	99.9666	460	468	95	conclusive
Fructobacillus fructosus	strain=NRIC 1058	GCA_001047095.2	1631	1631	type	True	99.9538	459	468	95	conclusive
Fructobacillus papyrifericola	strain=M1-21	GCA_018437235.1	2713172	2713172	type	True	83.3523	235	468	95	below_threshold
Fructobacillus parabroussonetiae	strain=S1-1	GCA_018437265.1	2713174	2713174	type	True	81.7574	217	468	95	below_threshold
Fructobacillus papyriferae	strain=M1-10	GCA_018437225.1	2713171	2713171	type	True	81.3662	196	468	95	below_threshold
Fructobacillus durionis	strain=DSM 19113	GCA_900112405.1	283737	283737	type	True	81.2031	232	468	95	below_threshold
Fructobacillus broussonetiae	strain=M2-14	GCA_018437275.1	2713173	2713173	type	True	80.9615	169	468	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:33,250] [INFO] DFAST Taxonomy check result was written to GCF_000185045.1_ASM18504v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:33,251] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:33,251] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:33,252] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0a0a77d-de3b-4b33-8231-167a0210bb91/dqc_reference/checkm_data
[2024-01-24 13:01:33,254] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:33,273] [INFO] Task started: CheckM
[2024-01-24 13:01:33,274] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000185045.1_ASM18504v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000185045.1_ASM18504v1_genomic.fna/checkm_input GCF_000185045.1_ASM18504v1_genomic.fna/checkm_result
[2024-01-24 13:01:52,486] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:52,487] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:52,503] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:52,504] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:52,504] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000185045.1_ASM18504v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:52,505] [INFO] Task started: Blastn
[2024-01-24 13:01:52,505] [INFO] Running command: blastn -query GCF_000185045.1_ASM18504v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0a0a77d-de3b-4b33-8231-167a0210bb91/dqc_reference/reference_markers_gtdb.fasta -out GCF_000185045.1_ASM18504v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:53,252] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:53,256] [INFO] Selected 12 target genomes.
[2024-01-24 13:01:53,257] [INFO] Target genome list was writen to GCF_000185045.1_ASM18504v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:53,267] [INFO] Task started: fastANI
[2024-01-24 13:01:53,267] [INFO] Running command: fastANI --query /var/lib/cwl/stg0d8a115c-4e4c-4082-9e00-2aabf131fb12/GCF_000185045.1_ASM18504v1_genomic.fna.gz --refList GCF_000185045.1_ASM18504v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000185045.1_ASM18504v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:57,250] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:57,262] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:01:57,262] [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_001438695.1	s__Fructobacillus fructosus	99.9666	460	468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.37	98.18	0.96	0.91	4	conclusive
GCF_018437235.1	s__Fructobacillus sp018437235	83.3523	235	468	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	81.7574	217	468	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	81.3307	197	468	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	81.2031	232	468	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	80.9374	170	468	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	79.6673	125	468	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:01:57,264] [INFO] GTDB search result was written to GCF_000185045.1_ASM18504v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:57,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:57,268] [INFO] DFAST_QC result json was written to GCF_000185045.1_ASM18504v1_genomic.fna/dqc_result.json
[2024-01-24 13:01:57,269] [INFO] DFAST_QC completed!
[2024-01-24 13:01:57,269] [INFO] Total running time: 0h0m33s