[2024-01-24 13:01:12,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:01:12,198] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:01:12,198] [INFO] DQC Reference Directory: /var/lib/cwl/stgea2a9814-5248-4e34-97f2-c932b13962c3/dqc_reference
[2024-01-24 13:01:13,599] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:01:13,600] [INFO] Task started: Prodigal
[2024-01-24 13:01:13,600] [INFO] Running command: gunzip -c /var/lib/cwl/stg67d7d07c-bba6-426c-b746-8a9ece70764f/GCF_000615445.1_ASM61544v1_genomic.fna.gz | prodigal -d GCF_000615445.1_ASM61544v1_genomic.fna/cds.fna -a GCF_000615445.1_ASM61544v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:01:17,039] [INFO] Task succeeded: Prodigal
[2024-01-24 13:01:17,040] [INFO] Task started: HMMsearch
[2024-01-24 13:01:17,040] [INFO] Running command: hmmsearch --tblout GCF_000615445.1_ASM61544v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgea2a9814-5248-4e34-97f2-c932b13962c3/dqc_reference/reference_markers.hmm GCF_000615445.1_ASM61544v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:01:17,312] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:01:17,314] [INFO] Found 6/6 markers.
[2024-01-24 13:01:17,336] [INFO] Query marker FASTA was written to GCF_000615445.1_ASM61544v1_genomic.fna/markers.fasta
[2024-01-24 13:01:17,336] [INFO] Task started: Blastn
[2024-01-24 13:01:17,336] [INFO] Running command: blastn -query GCF_000615445.1_ASM61544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea2a9814-5248-4e34-97f2-c932b13962c3/dqc_reference/reference_markers.fasta -out GCF_000615445.1_ASM61544v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:17,955] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:17,958] [INFO] Selected 19 target genomes.
[2024-01-24 13:01:17,958] [INFO] Target genome list was writen to GCF_000615445.1_ASM61544v1_genomic.fna/target_genomes.txt
[2024-01-24 13:01:17,977] [INFO] Task started: fastANI
[2024-01-24 13:01:17,977] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d7d07c-bba6-426c-b746-8a9ece70764f/GCF_000615445.1_ASM61544v1_genomic.fna.gz --refList GCF_000615445.1_ASM61544v1_genomic.fna/target_genomes.txt --output GCF_000615445.1_ASM61544v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:01:24,093] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:24,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgea2a9814-5248-4e34-97f2-c932b13962c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:01:24,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgea2a9814-5248-4e34-97f2-c932b13962c3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:01:24,106] [INFO] Found 15 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:01:24,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:01:24,107] [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
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	100.0	570	573	95	conclusive
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	99.9718	569	573	95	conclusive
Lactobacillus xujianguonis	strain=HT111-2	GCA_004009905.1	2495899	2495899	type	True	81.1379	261	573	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_004354545.1	83683	83683	type	True	81.0037	256	573	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_000178475.1	83683	83683	type	True	80.97	254	573	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	80.9208	259	573	95	below_threshold
Lactobacillus kitasatonis	strain=JCM 1039	GCA_000615285.1	237446	237446	type	True	80.6476	261	573	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	80.6143	262	573	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	80.5755	259	573	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_001435325.1	151781	151781	type	True	80.5617	246	573	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	80.5041	254	573	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	80.4958	253	573	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	80.3804	264	573	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	80.3707	262	573	95	below_threshold
Lactobacillus acidophilus	strain=CIP 76.13	GCA_000469705.1	1579	1579	type	True	80.2841	267	573	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:01:24,109] [INFO] DFAST Taxonomy check result was written to GCF_000615445.1_ASM61544v1_genomic.fna/tc_result.tsv
[2024-01-24 13:01:24,109] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:01:24,109] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:01:24,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgea2a9814-5248-4e34-97f2-c932b13962c3/dqc_reference/checkm_data
[2024-01-24 13:01:24,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:01:24,135] [INFO] Task started: CheckM
[2024-01-24 13:01:24,136] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000615445.1_ASM61544v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000615445.1_ASM61544v1_genomic.fna/checkm_input GCF_000615445.1_ASM61544v1_genomic.fna/checkm_result
[2024-01-24 13:01:42,069] [INFO] Task succeeded: CheckM
[2024-01-24 13:01:42,071] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:01:42,090] [INFO] ===== Completeness check finished =====
[2024-01-24 13:01:42,091] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:01:42,091] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000615445.1_ASM61544v1_genomic.fna/markers.fasta)
[2024-01-24 13:01:42,091] [INFO] Task started: Blastn
[2024-01-24 13:01:42,091] [INFO] Running command: blastn -query GCF_000615445.1_ASM61544v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgea2a9814-5248-4e34-97f2-c932b13962c3/dqc_reference/reference_markers_gtdb.fasta -out GCF_000615445.1_ASM61544v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:01:42,890] [INFO] Task succeeded: Blastn
[2024-01-24 13:01:42,899] [INFO] Selected 15 target genomes.
[2024-01-24 13:01:42,899] [INFO] Target genome list was writen to GCF_000615445.1_ASM61544v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:01:42,909] [INFO] Task started: fastANI
[2024-01-24 13:01:42,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg67d7d07c-bba6-426c-b746-8a9ece70764f/GCF_000615445.1_ASM61544v1_genomic.fna.gz --refList GCF_000615445.1_ASM61544v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000615445.1_ASM61544v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:01:48,703] [INFO] Task succeeded: fastANI
[2024-01-24 13:01:48,716] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:01:48,716] [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_000615445.1	s__Lactobacillus hamsteri	100.0	570	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	conclusive
GCA_014803915.1	s__Lactobacillus sp014803915	81.7847	216	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004009905.1	s__Lactobacillus xujianguonis	81.1379	261	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_000178475.1	s__Lactobacillus amylolyticus	80.9698	255	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.45	98.00	0.96	0.87	8	-
GCF_001434335.1	s__Lactobacillus kalixensis	80.7491	269	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000615285.1	s__Lactobacillus kitasatonis	80.6476	261	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_000160855.1	s__Lactobacillus helveticus	80.6377	267	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001434975.1	s__Lactobacillus gallinarum	80.6104	275	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001435325.1	s__Lactobacillus intestinalis	80.5542	247	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.33	96.07	0.89	0.82	9	-
GCF_001436305.1	s__Lactobacillus ultunensis	80.4958	253	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_001591845.1	s__Lactobacillus acidophilus	80.3374	266	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_018987235.1	s__Lactobacillus crispatus	80.3141	257	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCA_018883635.1	s__Lactobacillus pullistercoris	80.2516	242	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570935.1	s__Lactobacillus sp007570935	80.0073	253	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000970855.1	s__Lactobacillus helsingborgensis	77.9974	115	573	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.65	97.05	0.93	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:01:48,718] [INFO] GTDB search result was written to GCF_000615445.1_ASM61544v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:01:48,719] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:01:48,723] [INFO] DFAST_QC result json was written to GCF_000615445.1_ASM61544v1_genomic.fna/dqc_result.json
[2024-01-24 13:01:48,723] [INFO] DFAST_QC completed!
[2024-01-24 13:01:48,724] [INFO] Total running time: 0h0m37s