[2023-06-13 19:40:31,901] [INFO] DFAST_QC pipeline started.
[2023-06-13 19:40:31,903] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 19:40:31,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg6ba2eee4-3737-463b-9f6e-3b083d616213/dqc_reference
[2023-06-13 19:40:33,036] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 19:40:33,037] [INFO] Task started: Prodigal
[2023-06-13 19:40:33,038] [INFO] Running command: gunzip -c /var/lib/cwl/stgabc93a8e-adb1-4abc-9912-ea76f4c57db1/GCA_022753435.1_ASM2275343v1_genomic.fna.gz | prodigal -d GCA_022753435.1_ASM2275343v1_genomic.fna/cds.fna -a GCA_022753435.1_ASM2275343v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 19:40:34,365] [INFO] Task succeeded: Prodigal
[2023-06-13 19:40:34,365] [INFO] Task started: HMMsearch
[2023-06-13 19:40:34,365] [INFO] Running command: hmmsearch --tblout GCA_022753435.1_ASM2275343v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6ba2eee4-3737-463b-9f6e-3b083d616213/dqc_reference/reference_markers.hmm GCA_022753435.1_ASM2275343v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 19:40:34,478] [INFO] Task succeeded: HMMsearch
[2023-06-13 19:40:34,479] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgabc93a8e-adb1-4abc-9912-ea76f4c57db1/GCA_022753435.1_ASM2275343v1_genomic.fna.gz]
[2023-06-13 19:40:34,490] [INFO] Query marker FASTA was written to GCA_022753435.1_ASM2275343v1_genomic.fna/markers.fasta
[2023-06-13 19:40:34,490] [INFO] Task started: Blastn
[2023-06-13 19:40:34,491] [INFO] Running command: blastn -query GCA_022753435.1_ASM2275343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba2eee4-3737-463b-9f6e-3b083d616213/dqc_reference/reference_markers.fasta -out GCA_022753435.1_ASM2275343v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:40:34,974] [INFO] Task succeeded: Blastn
[2023-06-13 19:40:34,978] [INFO] Selected 6 target genomes.
[2023-06-13 19:40:34,978] [INFO] Target genome list was writen to GCA_022753435.1_ASM2275343v1_genomic.fna/target_genomes.txt
[2023-06-13 19:40:34,979] [INFO] Task started: fastANI
[2023-06-13 19:40:34,979] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc93a8e-adb1-4abc-9912-ea76f4c57db1/GCA_022753435.1_ASM2275343v1_genomic.fna.gz --refList GCA_022753435.1_ASM2275343v1_genomic.fna/target_genomes.txt --output GCA_022753435.1_ASM2275343v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 19:40:36,595] [INFO] Task succeeded: fastANI
[2023-06-13 19:40:36,595] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6ba2eee4-3737-463b-9f6e-3b083d616213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 19:40:36,595] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6ba2eee4-3737-463b-9f6e-3b083d616213/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 19:40:36,602] [INFO] Found 6 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 19:40:36,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 19:40:36,603] [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=DSM 20584	GCA_001434005.1	47770	47770	type	True	97.4675	169	223	95	conclusive
Lactobacillus crispatus	strain=NCK2488	GCA_008694755.1	47770	47770	type	True	97.3395	169	223	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	97.3031	169	223	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	97.2125	175	223	95	conclusive
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	82.5433	113	223	95	below_threshold
Lactobacillus kefiranofaciens	strain=ATCC 43761	GCA_900103655.1	267818	267818	type	True	81.8838	121	223	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 19:40:36,605] [INFO] DFAST Taxonomy check result was written to GCA_022753435.1_ASM2275343v1_genomic.fna/tc_result.tsv
[2023-06-13 19:40:36,605] [INFO] ===== Taxonomy check completed =====
[2023-06-13 19:40:36,606] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 19:40:36,606] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6ba2eee4-3737-463b-9f6e-3b083d616213/dqc_reference/checkm_data
[2023-06-13 19:40:36,607] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 19:40:36,617] [INFO] Task started: CheckM
[2023-06-13 19:40:36,618] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022753435.1_ASM2275343v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022753435.1_ASM2275343v1_genomic.fna/checkm_input GCA_022753435.1_ASM2275343v1_genomic.fna/checkm_result
[2023-06-13 19:40:48,341] [INFO] Task succeeded: CheckM
[2023-06-13 19:40:48,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 19:40:48,359] [INFO] ===== Completeness check finished =====
[2023-06-13 19:40:48,360] [INFO] ===== Start GTDB Search =====
[2023-06-13 19:40:48,360] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022753435.1_ASM2275343v1_genomic.fna/markers.fasta)
[2023-06-13 19:40:48,360] [INFO] Task started: Blastn
[2023-06-13 19:40:48,360] [INFO] Running command: blastn -query GCA_022753435.1_ASM2275343v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6ba2eee4-3737-463b-9f6e-3b083d616213/dqc_reference/reference_markers_gtdb.fasta -out GCA_022753435.1_ASM2275343v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 19:40:48,846] [INFO] Task succeeded: Blastn
[2023-06-13 19:40:48,850] [INFO] Selected 8 target genomes.
[2023-06-13 19:40:48,850] [INFO] Target genome list was writen to GCA_022753435.1_ASM2275343v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 19:40:48,851] [INFO] Task started: fastANI
[2023-06-13 19:40:48,851] [INFO] Running command: fastANI --query /var/lib/cwl/stgabc93a8e-adb1-4abc-9912-ea76f4c57db1/GCA_022753435.1_ASM2275343v1_genomic.fna.gz --refList GCA_022753435.1_ASM2275343v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022753435.1_ASM2275343v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 19:40:51,273] [INFO] Task succeeded: fastANI
[2023-06-13 19:40:51,279] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 19:40:51,280] [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	97.2125	175	223	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	83.8169	112	223	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	83.3549	124	223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.43	96.81	0.87	0.78	24	-
GCF_000160855.1	s__Lactobacillus helveticus	82.7676	112	223	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	82.5287	115	223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
GCF_900103655.1	s__Lactobacillus kefiranofaciens	81.9236	119	223	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.62	99.18	0.95	0.85	9	-
--------------------------------------------------------------------------------
[2023-06-13 19:40:51,282] [INFO] GTDB search result was written to GCA_022753435.1_ASM2275343v1_genomic.fna/result_gtdb.tsv
[2023-06-13 19:40:51,282] [INFO] ===== GTDB Search completed =====
[2023-06-13 19:40:51,285] [INFO] DFAST_QC result json was written to GCA_022753435.1_ASM2275343v1_genomic.fna/dqc_result.json
[2023-06-13 19:40:51,285] [INFO] DFAST_QC completed!
[2023-06-13 19:40:51,285] [INFO] Total running time: 0h0m19s