[2023-06-13 14:45:47,650] [INFO] DFAST_QC pipeline started.
[2023-06-13 14:45:47,652] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 14:45:47,652] [INFO] DQC Reference Directory: /var/lib/cwl/stg716fa35c-e60b-42fd-8123-406541826fee/dqc_reference
[2023-06-13 14:45:48,841] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 14:45:48,842] [INFO] Task started: Prodigal
[2023-06-13 14:45:48,843] [INFO] Running command: gunzip -c /var/lib/cwl/stg1153ed69-0777-400e-91d8-7bcfd5eb627e/GCA_022756005.1_ASM2275600v1_genomic.fna.gz | prodigal -d GCA_022756005.1_ASM2275600v1_genomic.fna/cds.fna -a GCA_022756005.1_ASM2275600v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 14:45:50,329] [INFO] Task succeeded: Prodigal
[2023-06-13 14:45:50,329] [INFO] Task started: HMMsearch
[2023-06-13 14:45:50,330] [INFO] Running command: hmmsearch --tblout GCA_022756005.1_ASM2275600v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg716fa35c-e60b-42fd-8123-406541826fee/dqc_reference/reference_markers.hmm GCA_022756005.1_ASM2275600v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 14:45:50,525] [INFO] Task succeeded: HMMsearch
[2023-06-13 14:45:50,526] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg1153ed69-0777-400e-91d8-7bcfd5eb627e/GCA_022756005.1_ASM2275600v1_genomic.fna.gz]
[2023-06-13 14:45:50,541] [INFO] Query marker FASTA was written to GCA_022756005.1_ASM2275600v1_genomic.fna/markers.fasta
[2023-06-13 14:45:50,541] [INFO] Task started: Blastn
[2023-06-13 14:45:50,541] [INFO] Running command: blastn -query GCA_022756005.1_ASM2275600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg716fa35c-e60b-42fd-8123-406541826fee/dqc_reference/reference_markers.fasta -out GCA_022756005.1_ASM2275600v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:45:51,042] [INFO] Task succeeded: Blastn
[2023-06-13 14:45:51,045] [INFO] Selected 14 target genomes.
[2023-06-13 14:45:51,046] [INFO] Target genome list was writen to GCA_022756005.1_ASM2275600v1_genomic.fna/target_genomes.txt
[2023-06-13 14:45:51,047] [INFO] Task started: fastANI
[2023-06-13 14:45:51,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg1153ed69-0777-400e-91d8-7bcfd5eb627e/GCA_022756005.1_ASM2275600v1_genomic.fna.gz --refList GCA_022756005.1_ASM2275600v1_genomic.fna/target_genomes.txt --output GCA_022756005.1_ASM2275600v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 14:45:55,344] [INFO] Task succeeded: fastANI
[2023-06-13 14:45:55,345] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg716fa35c-e60b-42fd-8123-406541826fee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 14:45:55,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg716fa35c-e60b-42fd-8123-406541826fee/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 14:45:55,359] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2023-06-13 14:45:55,359] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 14:45:55,359] [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 iners	strain=DSM 13335	GCA_001435015.1	147802	147802	type	True	98.5917	236	265	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.5807	243	265	95	conclusive
Lactobacillus mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	77.4924	52	265	95	below_threshold
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	77.4828	51	265	95	below_threshold
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	77.4368	55	265	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	77.4347	52	265	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 14:45:55,361] [INFO] DFAST Taxonomy check result was written to GCA_022756005.1_ASM2275600v1_genomic.fna/tc_result.tsv
[2023-06-13 14:45:55,362] [INFO] ===== Taxonomy check completed =====
[2023-06-13 14:45:55,362] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 14:45:55,363] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg716fa35c-e60b-42fd-8123-406541826fee/dqc_reference/checkm_data
[2023-06-13 14:45:55,364] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 14:45:55,380] [INFO] Task started: CheckM
[2023-06-13 14:45:55,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022756005.1_ASM2275600v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022756005.1_ASM2275600v1_genomic.fna/checkm_input GCA_022756005.1_ASM2275600v1_genomic.fna/checkm_result
[2023-06-13 14:46:08,431] [INFO] Task succeeded: CheckM
[2023-06-13 14:46:08,433] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 14:46:08,456] [INFO] ===== Completeness check finished =====
[2023-06-13 14:46:08,456] [INFO] ===== Start GTDB Search =====
[2023-06-13 14:46:08,457] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022756005.1_ASM2275600v1_genomic.fna/markers.fasta)
[2023-06-13 14:46:08,457] [INFO] Task started: Blastn
[2023-06-13 14:46:08,457] [INFO] Running command: blastn -query GCA_022756005.1_ASM2275600v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg716fa35c-e60b-42fd-8123-406541826fee/dqc_reference/reference_markers_gtdb.fasta -out GCA_022756005.1_ASM2275600v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 14:46:08,927] [INFO] Task succeeded: Blastn
[2023-06-13 14:46:08,931] [INFO] Selected 16 target genomes.
[2023-06-13 14:46:08,931] [INFO] Target genome list was writen to GCA_022756005.1_ASM2275600v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 14:46:08,935] [INFO] Task started: fastANI
[2023-06-13 14:46:08,935] [INFO] Running command: fastANI --query /var/lib/cwl/stg1153ed69-0777-400e-91d8-7bcfd5eb627e/GCA_022756005.1_ASM2275600v1_genomic.fna.gz --refList GCA_022756005.1_ASM2275600v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022756005.1_ASM2275600v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 14:46:13,759] [INFO] Task succeeded: fastANI
[2023-06-13 14:46:13,764] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 14:46:13,765] [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_000160875.1	s__Lactobacillus iners	98.5807	243	265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.75	98.36	0.94	0.90	32	conclusive
GCF_007095465.1	s__Lactobacillus mulieris	77.4924	52	265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	-
GCF_001436455.1	s__Lactobacillus jensenii	77.4828	51	265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
GCF_001434975.1	s__Lactobacillus gallinarum	77.4347	52	265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.30	97.84	0.88	0.84	17	-
GCF_001591845.1	s__Lactobacillus acidophilus	77.2765	50	265	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
--------------------------------------------------------------------------------
[2023-06-13 14:46:13,767] [INFO] GTDB search result was written to GCA_022756005.1_ASM2275600v1_genomic.fna/result_gtdb.tsv
[2023-06-13 14:46:13,767] [INFO] ===== GTDB Search completed =====
[2023-06-13 14:46:13,770] [INFO] DFAST_QC result json was written to GCA_022756005.1_ASM2275600v1_genomic.fna/dqc_result.json
[2023-06-13 14:46:13,770] [INFO] DFAST_QC completed!
[2023-06-13 14:46:13,771] [INFO] Total running time: 0h0m26s