[2023-06-13 10:21:25,285] [INFO] DFAST_QC pipeline started.
[2023-06-13 10:21:25,286] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 10:21:25,287] [INFO] DQC Reference Directory: /var/lib/cwl/stgdc9157ea-5ca6-4ad2-ae20-b263181566d5/dqc_reference
[2023-06-13 10:21:26,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 10:21:26,462] [INFO] Task started: Prodigal
[2023-06-13 10:21:26,462] [INFO] Running command: gunzip -c /var/lib/cwl/stgbff9693c-4e27-4e9e-926f-f57bd0b4baf5/GCA_022643115.1_ASM2264311v1_genomic.fna.gz | prodigal -d GCA_022643115.1_ASM2264311v1_genomic.fna/cds.fna -a GCA_022643115.1_ASM2264311v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 10:21:30,428] [INFO] Task succeeded: Prodigal
[2023-06-13 10:21:30,428] [INFO] Task started: HMMsearch
[2023-06-13 10:21:30,428] [INFO] Running command: hmmsearch --tblout GCA_022643115.1_ASM2264311v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdc9157ea-5ca6-4ad2-ae20-b263181566d5/dqc_reference/reference_markers.hmm GCA_022643115.1_ASM2264311v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 10:21:30,606] [INFO] Task succeeded: HMMsearch
[2023-06-13 10:21:30,607] [INFO] Found 6/6 markers.
[2023-06-13 10:21:30,629] [INFO] Query marker FASTA was written to GCA_022643115.1_ASM2264311v1_genomic.fna/markers.fasta
[2023-06-13 10:21:30,629] [INFO] Task started: Blastn
[2023-06-13 10:21:30,629] [INFO] Running command: blastn -query GCA_022643115.1_ASM2264311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc9157ea-5ca6-4ad2-ae20-b263181566d5/dqc_reference/reference_markers.fasta -out GCA_022643115.1_ASM2264311v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:21:31,179] [INFO] Task succeeded: Blastn
[2023-06-13 10:21:31,182] [INFO] Selected 13 target genomes.
[2023-06-13 10:21:31,183] [INFO] Target genome list was writen to GCA_022643115.1_ASM2264311v1_genomic.fna/target_genomes.txt
[2023-06-13 10:21:31,184] [INFO] Task started: fastANI
[2023-06-13 10:21:31,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff9693c-4e27-4e9e-926f-f57bd0b4baf5/GCA_022643115.1_ASM2264311v1_genomic.fna.gz --refList GCA_022643115.1_ASM2264311v1_genomic.fna/target_genomes.txt --output GCA_022643115.1_ASM2264311v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 10:21:36,118] [INFO] Task succeeded: fastANI
[2023-06-13 10:21:36,118] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdc9157ea-5ca6-4ad2-ae20-b263181566d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 10:21:36,119] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdc9157ea-5ca6-4ad2-ae20-b263181566d5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 10:21:36,129] [INFO] Found 11 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 10:21:36,129] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 10:21:36,129] [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=NCK2488	GCA_008694755.1	47770	47770	type	True	96.3898	489	688	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	96.3627	499	688	95	conclusive
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	96.3456	489	688	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	96.1674	529	688	95	conclusive
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	81.3017	342	688	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.2969	345	688	95	below_threshold
Lactobacillus amylovorus	strain=DSM 20531	GCA_002706375.1	1604	1604	type	True	81.286	372	688	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	81.0374	356	688	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.748	215	688	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.0094	94	688	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	77.7912	112	688	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 10:21:36,131] [INFO] DFAST Taxonomy check result was written to GCA_022643115.1_ASM2264311v1_genomic.fna/tc_result.tsv
[2023-06-13 10:21:36,132] [INFO] ===== Taxonomy check completed =====
[2023-06-13 10:21:36,132] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 10:21:36,132] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdc9157ea-5ca6-4ad2-ae20-b263181566d5/dqc_reference/checkm_data
[2023-06-13 10:21:36,133] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 10:21:36,156] [INFO] Task started: CheckM
[2023-06-13 10:21:36,157] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022643115.1_ASM2264311v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022643115.1_ASM2264311v1_genomic.fna/checkm_input GCA_022643115.1_ASM2264311v1_genomic.fna/checkm_result
[2023-06-13 10:21:54,516] [INFO] Task succeeded: CheckM
[2023-06-13 10:21:54,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 10:21:54,533] [INFO] ===== Completeness check finished =====
[2023-06-13 10:21:54,533] [INFO] ===== Start GTDB Search =====
[2023-06-13 10:21:54,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022643115.1_ASM2264311v1_genomic.fna/markers.fasta)
[2023-06-13 10:21:54,534] [INFO] Task started: Blastn
[2023-06-13 10:21:54,534] [INFO] Running command: blastn -query GCA_022643115.1_ASM2264311v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdc9157ea-5ca6-4ad2-ae20-b263181566d5/dqc_reference/reference_markers_gtdb.fasta -out GCA_022643115.1_ASM2264311v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 10:21:55,266] [INFO] Task succeeded: Blastn
[2023-06-13 10:21:55,270] [INFO] Selected 12 target genomes.
[2023-06-13 10:21:55,270] [INFO] Target genome list was writen to GCA_022643115.1_ASM2264311v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 10:21:55,272] [INFO] Task started: fastANI
[2023-06-13 10:21:55,272] [INFO] Running command: fastANI --query /var/lib/cwl/stgbff9693c-4e27-4e9e-926f-f57bd0b4baf5/GCA_022643115.1_ASM2264311v1_genomic.fna.gz --refList GCA_022643115.1_ASM2264311v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022643115.1_ASM2264311v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 10:21:59,745] [INFO] Task succeeded: fastANI
[2023-06-13 10:21:59,755] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 10:21:59,755] [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	96.1417	529	688	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_001434975.1	s__Lactobacillus gallinarum	82.002	341	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_000615285.1	s__Lactobacillus kitasatonis	81.7475	335	688	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	81.3426	370	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_001591845.1	s__Lactobacillus acidophilus	81.3138	341	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_000160855.1	s__Lactobacillus helveticus	81.2982	341	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_001436305.1	s__Lactobacillus ultunensis	81.2767	346	688	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	81.0245	345	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
GCA_014803905.1	s__Lactobacillus sp014803905	77.9078	55	688	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013346935.1	s__Lactobacillus melliventris	77.4473	80	688	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 10:21:59,757] [INFO] GTDB search result was written to GCA_022643115.1_ASM2264311v1_genomic.fna/result_gtdb.tsv
[2023-06-13 10:21:59,758] [INFO] ===== GTDB Search completed =====
[2023-06-13 10:21:59,761] [INFO] DFAST_QC result json was written to GCA_022643115.1_ASM2264311v1_genomic.fna/dqc_result.json
[2023-06-13 10:21:59,761] [INFO] DFAST_QC completed!
[2023-06-13 10:21:59,761] [INFO] Total running time: 0h0m34s