[2024-01-24 13:46:40,709] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:40,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:40,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg6d3edfd3-43d8-48e0-85ee-95c78b1df560/dqc_reference
[2024-01-24 13:46:42,061] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:42,062] [INFO] Task started: Prodigal
[2024-01-24 13:46:42,062] [INFO] Running command: gunzip -c /var/lib/cwl/stgc0ca311f-0a11-4d3f-9d41-032d6b4854c8/GCF_000615685.1_ASM61568v1_genomic.fna.gz | prodigal -d GCF_000615685.1_ASM61568v1_genomic.fna/cds.fna -a GCF_000615685.1_ASM61568v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:46,317] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:46,318] [INFO] Task started: HMMsearch
[2024-01-24 13:46:46,318] [INFO] Running command: hmmsearch --tblout GCF_000615685.1_ASM61568v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6d3edfd3-43d8-48e0-85ee-95c78b1df560/dqc_reference/reference_markers.hmm GCF_000615685.1_ASM61568v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:46,621] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:46,623] [INFO] Found 6/6 markers.
[2024-01-24 13:46:46,655] [INFO] Query marker FASTA was written to GCF_000615685.1_ASM61568v1_genomic.fna/markers.fasta
[2024-01-24 13:46:46,655] [INFO] Task started: Blastn
[2024-01-24 13:46:46,655] [INFO] Running command: blastn -query GCF_000615685.1_ASM61568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d3edfd3-43d8-48e0-85ee-95c78b1df560/dqc_reference/reference_markers.fasta -out GCF_000615685.1_ASM61568v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:47,268] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:47,321] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:47,322] [INFO] Target genome list was writen to GCF_000615685.1_ASM61568v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:47,472] [INFO] Task started: fastANI
[2024-01-24 13:46:47,473] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ca311f-0a11-4d3f-9d41-032d6b4854c8/GCF_000615685.1_ASM61568v1_genomic.fna.gz --refList GCF_000615685.1_ASM61568v1_genomic.fna/target_genomes.txt --output GCF_000615685.1_ASM61568v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:53,109] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:53,110] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6d3edfd3-43d8-48e0-85ee-95c78b1df560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:53,110] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6d3edfd3-43d8-48e0-85ee-95c78b1df560/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:53,121] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:46:53,121] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:53,121] [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 kefiranofaciens subsp. kefiranofaciens	strain=JCM 6985	GCA_000615685.1	190905	267818	type	True	100.0	687	692	95	conclusive
Lactobacillus kefiranofaciens	strain=ATCC 43761	GCA_900103655.1	267818	267818	type	True	99.9841	688	692	95	conclusive
Lactobacillus kefiranofaciens subsp. kefiranofaciens	strain=DSM 5016	GCA_001435275.1	190905	267818	type	True	99.9584	680	692	95	conclusive
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	99.408	576	692	95	conclusive
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	84.844	330	692	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	82.6427	362	692	95	below_threshold
Lactobacillus kitasatonis	strain=DSM 16761	GCA_001434435.1	237446	237446	type	True	81.9396	359	692	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_000159415.1	227945	227945	type	True	81.8661	396	692	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.7752	376	692	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.893	209	692	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	78.4513	96	692	95	below_threshold
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	77.6744	97	692	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:53,123] [INFO] DFAST Taxonomy check result was written to GCF_000615685.1_ASM61568v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:53,124] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:53,124] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:53,124] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6d3edfd3-43d8-48e0-85ee-95c78b1df560/dqc_reference/checkm_data
[2024-01-24 13:46:53,125] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:53,151] [INFO] Task started: CheckM
[2024-01-24 13:46:53,151] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000615685.1_ASM61568v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000615685.1_ASM61568v1_genomic.fna/checkm_input GCF_000615685.1_ASM61568v1_genomic.fna/checkm_result
[2024-01-24 13:47:14,360] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:14,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:14,384] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:14,385] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:14,385] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000615685.1_ASM61568v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:14,386] [INFO] Task started: Blastn
[2024-01-24 13:47:14,386] [INFO] Running command: blastn -query GCF_000615685.1_ASM61568v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6d3edfd3-43d8-48e0-85ee-95c78b1df560/dqc_reference/reference_markers_gtdb.fasta -out GCF_000615685.1_ASM61568v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:15,155] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:15,159] [INFO] Selected 11 target genomes.
[2024-01-24 13:47:15,159] [INFO] Target genome list was writen to GCF_000615685.1_ASM61568v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:15,169] [INFO] Task started: fastANI
[2024-01-24 13:47:15,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgc0ca311f-0a11-4d3f-9d41-032d6b4854c8/GCF_000615685.1_ASM61568v1_genomic.fna.gz --refList GCF_000615685.1_ASM61568v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000615685.1_ASM61568v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:19,978] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:19,996] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:19,997] [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_900103655.1	s__Lactobacillus kefiranofaciens	99.9841	688	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	conclusive
GCF_000160855.1	s__Lactobacillus helveticus	84.5889	384	692	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	82.586	365	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_002706375.1	s__Lactobacillus amylovorus	82.3767	362	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_000615285.1	s__Lactobacillus kitasatonis	81.9698	351	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_001436305.1	s__Lactobacillus ultunensis	81.8145	374	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_018987235.1	s__Lactobacillus crispatus	81.6635	353	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	-
GCF_001591845.1	s__Lactobacillus acidophilus	81.3229	339	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_000615445.1	s__Lactobacillus hamsteri	80.3132	233	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000296835.1	s__Lactobacillus hominis	78.7508	141	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	77.7073	95	692	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:19,999] [INFO] GTDB search result was written to GCF_000615685.1_ASM61568v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:20,000] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:20,004] [INFO] DFAST_QC result json was written to GCF_000615685.1_ASM61568v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:20,004] [INFO] DFAST_QC completed!
[2024-01-24 13:47:20,004] [INFO] Total running time: 0h0m39s