[2023-06-14 00:41:47,734] [INFO] DFAST_QC pipeline started.
[2023-06-14 00:41:47,740] [INFO] DFAST_QC version: 0.5.7
[2023-06-14 00:41:47,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg7b8b1a30-19ee-4f08-bc4e-83d0b676304f/dqc_reference
[2023-06-14 00:41:49,488] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-14 00:41:49,489] [INFO] Task started: Prodigal
[2023-06-14 00:41:49,489] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ea4c885-9bcc-432f-97b8-9ceccf469c78/GCA_022752155.1_ASM2275215v1_genomic.fna.gz | prodigal -d GCA_022752155.1_ASM2275215v1_genomic.fna/cds.fna -a GCA_022752155.1_ASM2275215v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-14 00:41:51,325] [INFO] Task succeeded: Prodigal
[2023-06-14 00:41:51,325] [INFO] Task started: HMMsearch
[2023-06-14 00:41:51,325] [INFO] Running command: hmmsearch --tblout GCA_022752155.1_ASM2275215v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7b8b1a30-19ee-4f08-bc4e-83d0b676304f/dqc_reference/reference_markers.hmm GCA_022752155.1_ASM2275215v1_genomic.fna/protein.faa > /dev/null
[2023-06-14 00:41:51,461] [INFO] Task succeeded: HMMsearch
[2023-06-14 00:41:51,462] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9ea4c885-9bcc-432f-97b8-9ceccf469c78/GCA_022752155.1_ASM2275215v1_genomic.fna.gz]
[2023-06-14 00:41:51,480] [INFO] Query marker FASTA was written to GCA_022752155.1_ASM2275215v1_genomic.fna/markers.fasta
[2023-06-14 00:41:51,481] [INFO] Task started: Blastn
[2023-06-14 00:41:51,481] [INFO] Running command: blastn -query GCA_022752155.1_ASM2275215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b8b1a30-19ee-4f08-bc4e-83d0b676304f/dqc_reference/reference_markers.fasta -out GCA_022752155.1_ASM2275215v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:41:53,150] [INFO] Task succeeded: Blastn
[2023-06-14 00:41:53,153] [INFO] Selected 7 target genomes.
[2023-06-14 00:41:53,153] [INFO] Target genome list was writen to GCA_022752155.1_ASM2275215v1_genomic.fna/target_genomes.txt
[2023-06-14 00:41:53,154] [INFO] Task started: fastANI
[2023-06-14 00:41:53,155] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea4c885-9bcc-432f-97b8-9ceccf469c78/GCA_022752155.1_ASM2275215v1_genomic.fna.gz --refList GCA_022752155.1_ASM2275215v1_genomic.fna/target_genomes.txt --output GCA_022752155.1_ASM2275215v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-14 00:41:55,806] [INFO] Task succeeded: fastANI
[2023-06-14 00:41:55,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7b8b1a30-19ee-4f08-bc4e-83d0b676304f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-14 00:41:55,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7b8b1a30-19ee-4f08-bc4e-83d0b676304f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-14 00:41:55,813] [INFO] Found 7 fastANI hits (4 hits with ANI > threshold)
[2023-06-14 00:41:55,813] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-14 00:41:55,813] [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	97.5962	275	336	95	conclusive
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	97.5521	284	336	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	97.4939	283	336	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	97.488	291	336	95	conclusive
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	81.8288	190	336	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.6795	195	336	95	below_threshold
Lactobacillus kefiranofaciens	strain=ATCC 43761	GCA_900103655.1	267818	267818	type	True	81.4297	190	336	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-14 00:41:55,815] [INFO] DFAST Taxonomy check result was written to GCA_022752155.1_ASM2275215v1_genomic.fna/tc_result.tsv
[2023-06-14 00:41:55,815] [INFO] ===== Taxonomy check completed =====
[2023-06-14 00:41:55,815] [INFO] ===== Start completeness check using CheckM =====
[2023-06-14 00:41:55,815] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7b8b1a30-19ee-4f08-bc4e-83d0b676304f/dqc_reference/checkm_data
[2023-06-14 00:41:55,816] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-14 00:41:55,831] [INFO] Task started: CheckM
[2023-06-14 00:41:55,831] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022752155.1_ASM2275215v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022752155.1_ASM2275215v1_genomic.fna/checkm_input GCA_022752155.1_ASM2275215v1_genomic.fna/checkm_result
[2023-06-14 00:42:09,955] [INFO] Task succeeded: CheckM
[2023-06-14 00:42:09,956] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-14 00:42:09,984] [INFO] ===== Completeness check finished =====
[2023-06-14 00:42:09,984] [INFO] ===== Start GTDB Search =====
[2023-06-14 00:42:09,984] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022752155.1_ASM2275215v1_genomic.fna/markers.fasta)
[2023-06-14 00:42:09,984] [INFO] Task started: Blastn
[2023-06-14 00:42:09,984] [INFO] Running command: blastn -query GCA_022752155.1_ASM2275215v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7b8b1a30-19ee-4f08-bc4e-83d0b676304f/dqc_reference/reference_markers_gtdb.fasta -out GCA_022752155.1_ASM2275215v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-14 00:42:10,513] [INFO] Task succeeded: Blastn
[2023-06-14 00:42:10,516] [INFO] Selected 10 target genomes.
[2023-06-14 00:42:10,516] [INFO] Target genome list was writen to GCA_022752155.1_ASM2275215v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-14 00:42:10,517] [INFO] Task started: fastANI
[2023-06-14 00:42:10,517] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ea4c885-9bcc-432f-97b8-9ceccf469c78/GCA_022752155.1_ASM2275215v1_genomic.fna.gz --refList GCA_022752155.1_ASM2275215v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022752155.1_ASM2275215v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-14 00:42:14,195] [INFO] Task succeeded: fastANI
[2023-06-14 00:42:14,203] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-14 00:42:14,203] [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	97.488	291	336	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	83.04	196	336	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	82.5738	199	336	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	82.5653	213	336	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	82.0113	191	336	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	81.9345	191	336	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	81.678	195	336	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	81.4372	189	336	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	78.346	71	336	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	77.9514	54	336	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.75	96.46	0.90	0.86	9	-
--------------------------------------------------------------------------------
[2023-06-14 00:42:14,205] [INFO] GTDB search result was written to GCA_022752155.1_ASM2275215v1_genomic.fna/result_gtdb.tsv
[2023-06-14 00:42:14,205] [INFO] ===== GTDB Search completed =====
[2023-06-14 00:42:14,208] [INFO] DFAST_QC result json was written to GCA_022752155.1_ASM2275215v1_genomic.fna/dqc_result.json
[2023-06-14 00:42:14,208] [INFO] DFAST_QC completed!
[2023-06-14 00:42:14,208] [INFO] Total running time: 0h0m26s