[2024-01-24 11:12:36,238] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:12:36,244] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:12:36,244] [INFO] DQC Reference Directory: /var/lib/cwl/stg293b0be2-2449-4ab7-a827-159d5a328f31/dqc_reference
[2024-01-24 11:12:38,661] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:12:38,662] [INFO] Task started: Prodigal
[2024-01-24 11:12:38,662] [INFO] Running command: gunzip -c /var/lib/cwl/stg6227b857-ef38-4a7d-bfbd-7aba9908b33a/GCF_003096575.1_ASM309657v1_genomic.fna.gz | prodigal -d GCF_003096575.1_ASM309657v1_genomic.fna/cds.fna -a GCF_003096575.1_ASM309657v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:12:41,992] [INFO] Task succeeded: Prodigal
[2024-01-24 11:12:41,993] [INFO] Task started: HMMsearch
[2024-01-24 11:12:41,993] [INFO] Running command: hmmsearch --tblout GCF_003096575.1_ASM309657v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg293b0be2-2449-4ab7-a827-159d5a328f31/dqc_reference/reference_markers.hmm GCF_003096575.1_ASM309657v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:12:42,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:12:42,159] [INFO] Found 6/6 markers.
[2024-01-24 11:12:42,175] [INFO] Query marker FASTA was written to GCF_003096575.1_ASM309657v1_genomic.fna/markers.fasta
[2024-01-24 11:12:42,175] [INFO] Task started: Blastn
[2024-01-24 11:12:42,175] [INFO] Running command: blastn -query GCF_003096575.1_ASM309657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293b0be2-2449-4ab7-a827-159d5a328f31/dqc_reference/reference_markers.fasta -out GCF_003096575.1_ASM309657v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:12:43,163] [INFO] Task succeeded: Blastn
[2024-01-24 11:12:43,167] [INFO] Selected 25 target genomes.
[2024-01-24 11:12:43,167] [INFO] Target genome list was writen to GCF_003096575.1_ASM309657v1_genomic.fna/target_genomes.txt
[2024-01-24 11:12:43,351] [INFO] Task started: fastANI
[2024-01-24 11:12:43,351] [INFO] Running command: fastANI --query /var/lib/cwl/stg6227b857-ef38-4a7d-bfbd-7aba9908b33a/GCF_003096575.1_ASM309657v1_genomic.fna.gz --refList GCF_003096575.1_ASM309657v1_genomic.fna/target_genomes.txt --output GCF_003096575.1_ASM309657v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:12:51,611] [INFO] Task succeeded: fastANI
[2024-01-24 11:12:51,612] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg293b0be2-2449-4ab7-a827-159d5a328f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:12:51,612] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg293b0be2-2449-4ab7-a827-159d5a328f31/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:12:51,627] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:12:51,627] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:12:51,628] [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
Convivina intestini	strain=DSM 28795	GCA_003096575.1	1505726	1505726	type	True	100.0	519	521	95	conclusive
Fructobacillus fructosus	strain=DSM 20349	GCA_001438695.1	1631	1631	type	True	79.0362	68	521	95	below_threshold
Fructobacillus fructosus	strain=KCTC 3544	GCA_000185045.2	1631	1631	type	True	79.0188	65	521	95	below_threshold
Fructobacillus fructosus	strain=NRIC 1058	GCA_001047095.2	1631	1631	type	True	78.9886	66	521	95	below_threshold
Fructobacillus durionis	strain=DSM 19113	GCA_900112405.1	283737	283737	type	True	78.5081	71	521	95	below_threshold
Leuconostoc kimchii	strain=IMSNU 11154	GCA_000092505.1	136609	136609	type	True	78.3926	63	521	95	below_threshold
Leuconostoc miyukkimchii	strain=JCM 17445	GCA_019656055.1	910540	910540	type	True	78.3056	58	521	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_016908715.1	1406906	1406906	type	True	78.1626	68	521	95	below_threshold
Leuconostoc rapi	strain=DSM 27776	GCA_019656095.1	1406906	1406906	type	True	78.1335	67	521	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_020089505.1	1607837	1244	type	True	77.8836	56	521	95	below_threshold
Leuconostoc gelidum subsp. aenigmaticum	strain=DSM 19375	GCA_019655935.1	1607837	1244	type	True	77.7267	56	521	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=NBRC 113245	GCA_019655955.1	115778	1244	type	True	77.6728	61	521	95	below_threshold
Leuconostoc inhae	strain=DSM 15101	GCA_019656015.1	178001	178001	suspected-type	True	77.5601	62	521	95	below_threshold
Leuconostoc gelidum subsp. gasicomitatum	strain=type strain: LMG 18811	GCA_000196855.1	115778	1244	type	True	77.4695	63	521	95	below_threshold
Leuconostoc gelidum subsp. gelidum	strain=KCTC 3527	GCA_000166715.2	1607839	1244	type	True	77.4186	63	521	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:12:51,629] [INFO] DFAST Taxonomy check result was written to GCF_003096575.1_ASM309657v1_genomic.fna/tc_result.tsv
[2024-01-24 11:12:51,630] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:12:51,630] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:12:51,630] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg293b0be2-2449-4ab7-a827-159d5a328f31/dqc_reference/checkm_data
[2024-01-24 11:12:51,632] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:12:51,650] [INFO] Task started: CheckM
[2024-01-24 11:12:51,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003096575.1_ASM309657v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003096575.1_ASM309657v1_genomic.fna/checkm_input GCF_003096575.1_ASM309657v1_genomic.fna/checkm_result
[2024-01-24 11:13:08,118] [INFO] Task succeeded: CheckM
[2024-01-24 11:13:08,119] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:13:08,138] [INFO] ===== Completeness check finished =====
[2024-01-24 11:13:08,138] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:13:08,139] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003096575.1_ASM309657v1_genomic.fna/markers.fasta)
[2024-01-24 11:13:08,139] [INFO] Task started: Blastn
[2024-01-24 11:13:08,139] [INFO] Running command: blastn -query GCF_003096575.1_ASM309657v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg293b0be2-2449-4ab7-a827-159d5a328f31/dqc_reference/reference_markers_gtdb.fasta -out GCF_003096575.1_ASM309657v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:13:08,933] [INFO] Task succeeded: Blastn
[2024-01-24 11:13:08,936] [INFO] Selected 22 target genomes.
[2024-01-24 11:13:08,936] [INFO] Target genome list was writen to GCF_003096575.1_ASM309657v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:13:08,960] [INFO] Task started: fastANI
[2024-01-24 11:13:08,960] [INFO] Running command: fastANI --query /var/lib/cwl/stg6227b857-ef38-4a7d-bfbd-7aba9908b33a/GCF_003096575.1_ASM309657v1_genomic.fna.gz --refList GCF_003096575.1_ASM309657v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003096575.1_ASM309657v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:13:15,947] [INFO] Task succeeded: fastANI
[2024-01-24 11:13:15,956] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:13:15,956] [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_003096575.1	s__Convivina intestini	100.0	519	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Convivina	95.0	99.99	99.99	0.99	0.99	2	conclusive
GCF_001438695.1	s__Fructobacillus fructosus	79.0362	68	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.37	98.18	0.96	0.91	4	-
GCF_001038455.1	s__Fructobacillus sp001038455	78.6653	85	521	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	78.5081	71	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092505.1	s__Leuconostoc kimchii	78.3943	63	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	99.55	99.53	0.95	0.95	3	-
GCF_900108455.1	s__Fructobacillus pseudoficulneus	78.2279	95	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Fructobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_016908715.1	s__Leuconostoc rapi	78.1626	68	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009676745.1	s__Leuconostoc mesenteroides_B	78.1333	71	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	100.00	100.00	0.99	0.99	2	-
GCF_000166715.1	s__Leuconostoc gelidum	77.468	62	521	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Leuconostoc	95.0	98.91	98.75	0.91	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 11:13:15,957] [INFO] GTDB search result was written to GCF_003096575.1_ASM309657v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:13:15,958] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:13:15,961] [INFO] DFAST_QC result json was written to GCF_003096575.1_ASM309657v1_genomic.fna/dqc_result.json
[2024-01-24 11:13:15,961] [INFO] DFAST_QC completed!
[2024-01-24 11:13:15,961] [INFO] Total running time: 0h0m40s