[2023-06-13 00:23:28,682] [INFO] DFAST_QC pipeline started.
[2023-06-13 00:23:28,684] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 00:23:28,684] [INFO] DQC Reference Directory: /var/lib/cwl/stg32486059-73c3-422d-9ffc-ebfab91cc69a/dqc_reference
[2023-06-13 00:23:29,948] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 00:23:29,949] [INFO] Task started: Prodigal
[2023-06-13 00:23:29,949] [INFO] Running command: gunzip -c /var/lib/cwl/stg6171dc0c-3e17-4a21-9e4d-41bcb224d9cb/GCA_022755065.1_ASM2275506v1_genomic.fna.gz | prodigal -d GCA_022755065.1_ASM2275506v1_genomic.fna/cds.fna -a GCA_022755065.1_ASM2275506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 00:23:32,621] [INFO] Task succeeded: Prodigal
[2023-06-13 00:23:32,621] [INFO] Task started: HMMsearch
[2023-06-13 00:23:32,621] [INFO] Running command: hmmsearch --tblout GCA_022755065.1_ASM2275506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg32486059-73c3-422d-9ffc-ebfab91cc69a/dqc_reference/reference_markers.hmm GCA_022755065.1_ASM2275506v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 00:23:32,842] [INFO] Task succeeded: HMMsearch
[2023-06-13 00:23:32,843] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6171dc0c-3e17-4a21-9e4d-41bcb224d9cb/GCA_022755065.1_ASM2275506v1_genomic.fna.gz]
[2023-06-13 00:23:32,862] [INFO] Query marker FASTA was written to GCA_022755065.1_ASM2275506v1_genomic.fna/markers.fasta
[2023-06-13 00:23:32,862] [INFO] Task started: Blastn
[2023-06-13 00:23:32,863] [INFO] Running command: blastn -query GCA_022755065.1_ASM2275506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32486059-73c3-422d-9ffc-ebfab91cc69a/dqc_reference/reference_markers.fasta -out GCA_022755065.1_ASM2275506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:23:33,391] [INFO] Task succeeded: Blastn
[2023-06-13 00:23:33,396] [INFO] Selected 11 target genomes.
[2023-06-13 00:23:33,397] [INFO] Target genome list was writen to GCA_022755065.1_ASM2275506v1_genomic.fna/target_genomes.txt
[2023-06-13 00:23:33,405] [INFO] Task started: fastANI
[2023-06-13 00:23:33,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg6171dc0c-3e17-4a21-9e4d-41bcb224d9cb/GCA_022755065.1_ASM2275506v1_genomic.fna.gz --refList GCA_022755065.1_ASM2275506v1_genomic.fna/target_genomes.txt --output GCA_022755065.1_ASM2275506v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 00:23:37,749] [INFO] Task succeeded: fastANI
[2023-06-13 00:23:37,749] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg32486059-73c3-422d-9ffc-ebfab91cc69a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 00:23:37,749] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg32486059-73c3-422d-9ffc-ebfab91cc69a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 00:23:37,759] [INFO] Found 9 fastANI hits (4 hits with ANI > threshold)
[2023-06-13 00:23:37,759] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 00:23:37,760] [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	97.7683	326	412	95	conclusive
Lactobacillus crispatus	strain=DSM 20584	GCA_001434005.1	47770	47770	type	True	97.6656	330	412	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_002088015.1	47770	47770	type	True	97.6311	332	412	95	conclusive
Lactobacillus crispatus	strain=ATCC 33820	GCA_018987235.1	47770	47770	suspected-type	True	97.5152	355	412	95	conclusive
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	81.5238	232	412	95	below_threshold
Lactobacillus ultunensis	strain=DSM 16047	GCA_001436305.1	227945	227945	type	True	81.3927	232	412	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	79.4871	163	412	95	below_threshold
Lactobacillus rodentium	strain=DSM 24759	GCA_024622425.1	947835	947835	type	True	78.4859	70	412	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	77.7588	88	412	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 00:23:37,765] [INFO] DFAST Taxonomy check result was written to GCA_022755065.1_ASM2275506v1_genomic.fna/tc_result.tsv
[2023-06-13 00:23:37,765] [INFO] ===== Taxonomy check completed =====
[2023-06-13 00:23:37,766] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 00:23:37,766] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg32486059-73c3-422d-9ffc-ebfab91cc69a/dqc_reference/checkm_data
[2023-06-13 00:23:37,768] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 00:23:37,794] [INFO] Task started: CheckM
[2023-06-13 00:23:37,794] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022755065.1_ASM2275506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022755065.1_ASM2275506v1_genomic.fna/checkm_input GCA_022755065.1_ASM2275506v1_genomic.fna/checkm_result
[2023-06-13 00:23:54,740] [INFO] Task succeeded: CheckM
[2023-06-13 00:23:54,741] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 00:23:54,779] [INFO] ===== Completeness check finished =====
[2023-06-13 00:23:54,780] [INFO] ===== Start GTDB Search =====
[2023-06-13 00:23:54,780] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022755065.1_ASM2275506v1_genomic.fna/markers.fasta)
[2023-06-13 00:23:54,780] [INFO] Task started: Blastn
[2023-06-13 00:23:54,780] [INFO] Running command: blastn -query GCA_022755065.1_ASM2275506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg32486059-73c3-422d-9ffc-ebfab91cc69a/dqc_reference/reference_markers_gtdb.fasta -out GCA_022755065.1_ASM2275506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 00:23:55,421] [INFO] Task succeeded: Blastn
[2023-06-13 00:23:55,429] [INFO] Selected 7 target genomes.
[2023-06-13 00:23:55,430] [INFO] Target genome list was writen to GCA_022755065.1_ASM2275506v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 00:23:55,437] [INFO] Task started: fastANI
[2023-06-13 00:23:55,437] [INFO] Running command: fastANI --query /var/lib/cwl/stg6171dc0c-3e17-4a21-9e4d-41bcb224d9cb/GCA_022755065.1_ASM2275506v1_genomic.fna.gz --refList GCA_022755065.1_ASM2275506v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022755065.1_ASM2275506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 00:23:58,312] [INFO] Task succeeded: fastANI
[2023-06-13 00:23:58,321] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 00:23:58,321] [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	97.4102	357	412	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	82.4336	230	412	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	82.4251	221	412	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	82.1574	234	412	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	81.9016	220	412	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	81.5659	226	412	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	81.4124	231	412	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 00:23:58,334] [INFO] GTDB search result was written to GCA_022755065.1_ASM2275506v1_genomic.fna/result_gtdb.tsv
[2023-06-13 00:23:58,335] [INFO] ===== GTDB Search completed =====
[2023-06-13 00:23:58,342] [INFO] DFAST_QC result json was written to GCA_022755065.1_ASM2275506v1_genomic.fna/dqc_result.json
[2023-06-13 00:23:58,343] [INFO] DFAST_QC completed!
[2023-06-13 00:23:58,343] [INFO] Total running time: 0h0m30s