[2023-06-13 06:11:32,742] [INFO] DFAST_QC pipeline started.
[2023-06-13 06:11:32,744] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 06:11:32,744] [INFO] DQC Reference Directory: /var/lib/cwl/stgbeaabe87-0d8c-4b6d-9831-0ae7b9fe4d1d/dqc_reference
[2023-06-13 06:11:34,036] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 06:11:34,037] [INFO] Task started: Prodigal
[2023-06-13 06:11:34,037] [INFO] Running command: gunzip -c /var/lib/cwl/stg22258da6-62f0-4d06-9915-9e98f8decfe4/GCA_022752345.1_ASM2275234v1_genomic.fna.gz | prodigal -d GCA_022752345.1_ASM2275234v1_genomic.fna/cds.fna -a GCA_022752345.1_ASM2275234v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 06:11:36,220] [INFO] Task succeeded: Prodigal
[2023-06-13 06:11:36,220] [INFO] Task started: HMMsearch
[2023-06-13 06:11:36,220] [INFO] Running command: hmmsearch --tblout GCA_022752345.1_ASM2275234v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbeaabe87-0d8c-4b6d-9831-0ae7b9fe4d1d/dqc_reference/reference_markers.hmm GCA_022752345.1_ASM2275234v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 06:11:36,429] [INFO] Task succeeded: HMMsearch
[2023-06-13 06:11:36,430] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg22258da6-62f0-4d06-9915-9e98f8decfe4/GCA_022752345.1_ASM2275234v1_genomic.fna.gz]
[2023-06-13 06:11:36,450] [INFO] Query marker FASTA was written to GCA_022752345.1_ASM2275234v1_genomic.fna/markers.fasta
[2023-06-13 06:11:36,450] [INFO] Task started: Blastn
[2023-06-13 06:11:36,451] [INFO] Running command: blastn -query GCA_022752345.1_ASM2275234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeaabe87-0d8c-4b6d-9831-0ae7b9fe4d1d/dqc_reference/reference_markers.fasta -out GCA_022752345.1_ASM2275234v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:36,965] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:36,969] [INFO] Selected 10 target genomes.
[2023-06-13 06:11:36,969] [INFO] Target genome list was writen to GCA_022752345.1_ASM2275234v1_genomic.fna/target_genomes.txt
[2023-06-13 06:11:36,972] [INFO] Task started: fastANI
[2023-06-13 06:11:36,972] [INFO] Running command: fastANI --query /var/lib/cwl/stg22258da6-62f0-4d06-9915-9e98f8decfe4/GCA_022752345.1_ASM2275234v1_genomic.fna.gz --refList GCA_022752345.1_ASM2275234v1_genomic.fna/target_genomes.txt --output GCA_022752345.1_ASM2275234v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 06:11:40,791] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:40,792] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbeaabe87-0d8c-4b6d-9831-0ae7b9fe4d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 06:11:40,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbeaabe87-0d8c-4b6d-9831-0ae7b9fe4d1d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 06:11:40,800] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 06:11:40,801] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 06:11:40,801] [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	97.8205	262	323	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	97.7938	273	323	95	conclusive
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	97.7815	265	323	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	97.7654	264	323	95	conclusive
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.0877	169	323	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.818	117	323	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	77.6914	57	323	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 06:11:40,804] [INFO] DFAST Taxonomy check result was written to GCA_022752345.1_ASM2275234v1_genomic.fna/tc_result.tsv
[2023-06-13 06:11:40,805] [INFO] ===== Taxonomy check completed =====
[2023-06-13 06:11:40,805] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 06:11:40,806] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbeaabe87-0d8c-4b6d-9831-0ae7b9fe4d1d/dqc_reference/checkm_data
[2023-06-13 06:11:40,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 06:11:40,826] [INFO] Task started: CheckM
[2023-06-13 06:11:40,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022752345.1_ASM2275234v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022752345.1_ASM2275234v1_genomic.fna/checkm_input GCA_022752345.1_ASM2275234v1_genomic.fna/checkm_result
[2023-06-13 06:11:55,987] [INFO] Task succeeded: CheckM
[2023-06-13 06:11:55,988] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 29.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 06:11:56,009] [INFO] ===== Completeness check finished =====
[2023-06-13 06:11:56,009] [INFO] ===== Start GTDB Search =====
[2023-06-13 06:11:56,010] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022752345.1_ASM2275234v1_genomic.fna/markers.fasta)
[2023-06-13 06:11:56,010] [INFO] Task started: Blastn
[2023-06-13 06:11:56,011] [INFO] Running command: blastn -query GCA_022752345.1_ASM2275234v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbeaabe87-0d8c-4b6d-9831-0ae7b9fe4d1d/dqc_reference/reference_markers_gtdb.fasta -out GCA_022752345.1_ASM2275234v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 06:11:56,472] [INFO] Task succeeded: Blastn
[2023-06-13 06:11:56,476] [INFO] Selected 7 target genomes.
[2023-06-13 06:11:56,476] [INFO] Target genome list was writen to GCA_022752345.1_ASM2275234v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 06:11:56,477] [INFO] Task started: fastANI
[2023-06-13 06:11:56,477] [INFO] Running command: fastANI --query /var/lib/cwl/stg22258da6-62f0-4d06-9915-9e98f8decfe4/GCA_022752345.1_ASM2275234v1_genomic.fna.gz --refList GCA_022752345.1_ASM2275234v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022752345.1_ASM2275234v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 06:11:58,833] [INFO] Task succeeded: fastANI
[2023-06-13 06:11:58,841] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 06:11:58,841] [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	97.7938	273	323	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	81.8533	178	323	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.87	97.76	0.93	0.87	3	-
GCF_001434975.1	s__Lactobacillus gallinarum	81.6752	179	323	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	81.4037	162	323	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.35	96.37	0.85	0.75	146	-
GCF_002706375.1	s__Lactobacillus amylovorus	81.3924	180	323	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	81.1325	167	323	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	81.0877	169	323	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.98	99.95	0.99	0.98	4	-
--------------------------------------------------------------------------------
[2023-06-13 06:11:58,843] [INFO] GTDB search result was written to GCA_022752345.1_ASM2275234v1_genomic.fna/result_gtdb.tsv
[2023-06-13 06:11:58,844] [INFO] ===== GTDB Search completed =====
[2023-06-13 06:11:58,847] [INFO] DFAST_QC result json was written to GCA_022752345.1_ASM2275234v1_genomic.fna/dqc_result.json
[2023-06-13 06:11:58,848] [INFO] DFAST_QC completed!
[2023-06-13 06:11:58,848] [INFO] Total running time: 0h0m26s