[2023-06-13 06:11:12,644] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:11:12,647] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:11:12,647] [INFO] DQC Reference Directory: /var/lib/cwl/stge9ba4717-3d8e-442a-a114-598765c183b3/dqc_reference
[2023-06-13 06:11:14,303] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:11:14,305] [INFO] Task started: Prodigal
[2023-06-13 06:11:14,305] [INFO] Running command: gunzip -c /var/lib/cwl/stgba20918c-f905-4dc2-aa5a-3b67db5e88ba/GCA_022758085.1_ASM2275808v1_genomic.fna.gz | prodigal -d GCA_022758085.1_ASM2275808v1_genomic.fna/cds.fna -a GCA_022758085.1_ASM2275808v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:11:17,840] [INFO] Task succeeded: Prodigal
[2023-06-13 06:11:17,840] [INFO] Task started: HMMsearch
[2023-06-13 06:11:17,840] [INFO] Running command: hmmsearch --tblout GCA_022758085.1_ASM2275808v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge9ba4717-3d8e-442a-a114-598765c183b3/dqc_reference/reference_markers.hmm GCA_022758085.1_ASM2275808v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:11:18,064] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:11:18,065] [INFO] Found 6/6 markers.
[2023-06-13 06:11:18,099] [INFO] Query marker FASTA was written to GCA_022758085.1_ASM2275808v1_genomic.fna/markers.fasta
[2023-06-13 06:11:18,100] [INFO] Task started: Blastn
[2023-06-13 06:11:18,100] [INFO] Running command: blastn -query GCA_022758085.1_ASM2275808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ba4717-3d8e-442a-a114-598765c183b3/dqc_reference/reference_markers.fasta -out GCA_022758085.1_ASM2275808v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:19,282] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:19,287] [INFO] Selected 13 target genomes.
[2023-06-13 06:11:19,287] [INFO] Target genome list was writen to GCA_022758085.1_ASM2275808v1_genomic.fna/target_genomes.txt
[2023-06-13 06:11:19,321] [INFO] Task started: fastANI
[2023-06-13 06:11:19,321] [INFO] Running command: fastANI --query /var/lib/cwl/stgba20918c-f905-4dc2-aa5a-3b67db5e88ba/GCA_022758085.1_ASM2275808v1_genomic.fna.gz --refList GCA_022758085.1_ASM2275808v1_genomic.fna/target_genomes.txt --output GCA_022758085.1_ASM2275808v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:11:24,095] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:24,095] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge9ba4717-3d8e-442a-a114-598765c183b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:11:24,096] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge9ba4717-3d8e-442a-a114-598765c183b3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:11:24,106] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 06:11:24,106] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 06:11:24,107] [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 crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	97.5257	432	538	95	conclusive
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	97.4199	431	538	95	conclusive
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	97.3755	432	538	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	97.2152	465	538	95	conclusive
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	81.6067	295	538	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.4481	297	538	95	below_threshold
Lactobacillus kefiranofaciens	strain=ATCC 43761	GCA_900103655.1	267818	267818	type	True	81.3037	302	538	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	81.2987	291	538	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.7623	190	538	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	77.9733	86	538	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	77.3798	100	538	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 06:11:24,109] [INFO] DFAST Taxonomy check result was written to GCA_022758085.1_ASM2275808v1_genomic.fna/tc_result.tsv
[2023-06-13 06:11:24,110] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:11:24,110] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:11:24,110] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge9ba4717-3d8e-442a-a114-598765c183b3/dqc_reference/checkm_data
[2023-06-13 06:11:24,111] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:11:24,141] [INFO] Task started: CheckM
[2023-06-13 06:11:24,142] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022758085.1_ASM2275808v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022758085.1_ASM2275808v1_genomic.fna/checkm_input GCA_022758085.1_ASM2275808v1_genomic.fna/checkm_result
[2023-06-13 06:11:42,806] [INFO] Task succeeded: CheckM
[2023-06-13 06:11:42,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:11:42,828] [INFO] ===== Completeness check finished =====
[2023-06-13 06:11:42,828] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:11:42,829] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022758085.1_ASM2275808v1_genomic.fna/markers.fasta)
[2023-06-13 06:11:42,829] [INFO] Task started: Blastn
[2023-06-13 06:11:42,829] [INFO] Running command: blastn -query GCA_022758085.1_ASM2275808v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge9ba4717-3d8e-442a-a114-598765c183b3/dqc_reference/reference_markers_gtdb.fasta -out GCA_022758085.1_ASM2275808v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:43,593] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:43,597] [INFO] Selected 10 target genomes.
[2023-06-13 06:11:43,597] [INFO] Target genome list was writen to GCA_022758085.1_ASM2275808v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:11:43,598] [INFO] Task started: fastANI
[2023-06-13 06:11:43,599] [INFO] Running command: fastANI --query /var/lib/cwl/stgba20918c-f905-4dc2-aa5a-3b67db5e88ba/GCA_022758085.1_ASM2275808v1_genomic.fna.gz --refList GCA_022758085.1_ASM2275808v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022758085.1_ASM2275808v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:11:47,379] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:47,392] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:11:47,392] [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_018987235.1	s__Lactobacillus crispatus	97.1666	466	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.75	96.25	0.84	0.70	161	conclusive
GCF_000615285.1	s__Lactobacillus kitasatonis	82.5344	300	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_002706375.1	s__Lactobacillus amylovorus	82.4864	309	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001434975.1	s__Lactobacillus gallinarum	82.4504	310	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000160855.1	s__Lactobacillus helveticus	81.8631	286	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001591845.1	s__Lactobacillus acidophilus	81.6604	289	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_001436305.1	s__Lactobacillus ultunensis	81.4233	298	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	81.3309	299	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCF_001436455.1	s__Lactobacillus jensenii	77.7432	107	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
GCF_013346935.1	s__Lactobacillus melliventris	77.135	77	538	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
--------------------------------------------------------------------------------
[2023-06-13 06:11:47,395] [INFO] GTDB search result was written to GCA_022758085.1_ASM2275808v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:11:47,395] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:11:47,399] [INFO] DFAST_QC result json was written to GCA_022758085.1_ASM2275808v1_genomic.fna/dqc_result.json
[2023-06-13 06:11:47,399] [INFO] DFAST_QC completed!
[2023-06-13 06:11:47,399] [INFO] Total running time: 0h0m35s