[2023-06-30 11:38:42,642] [INFO] DFAST_QC pipeline started.
[2023-06-30 11:38:42,644] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 11:38:42,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg86a58dca-c995-416f-94f5-7de2ec353dad/dqc_reference
[2023-06-30 11:38:43,786] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 11:38:43,787] [INFO] Task started: Prodigal
[2023-06-30 11:38:43,787] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d557184-770b-48c1-abaa-8f4a2ca583a4/GCA_025347245.1_ASM2534724v1_genomic.fna.gz | prodigal -d GCA_025347245.1_ASM2534724v1_genomic.fna/cds.fna -a GCA_025347245.1_ASM2534724v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 11:38:45,573] [INFO] Task succeeded: Prodigal
[2023-06-30 11:38:45,573] [INFO] Task started: HMMsearch
[2023-06-30 11:38:45,573] [INFO] Running command: hmmsearch --tblout GCA_025347245.1_ASM2534724v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg86a58dca-c995-416f-94f5-7de2ec353dad/dqc_reference/reference_markers.hmm GCA_025347245.1_ASM2534724v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 11:38:45,720] [INFO] Task succeeded: HMMsearch
[2023-06-30 11:38:45,721] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg2d557184-770b-48c1-abaa-8f4a2ca583a4/GCA_025347245.1_ASM2534724v1_genomic.fna.gz]
[2023-06-30 11:38:45,737] [INFO] Query marker FASTA was written to GCA_025347245.1_ASM2534724v1_genomic.fna/markers.fasta
[2023-06-30 11:38:45,737] [INFO] Task started: Blastn
[2023-06-30 11:38:45,737] [INFO] Running command: blastn -query GCA_025347245.1_ASM2534724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86a58dca-c995-416f-94f5-7de2ec353dad/dqc_reference/reference_markers.fasta -out GCA_025347245.1_ASM2534724v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:38:46,303] [INFO] Task succeeded: Blastn
[2023-06-30 11:38:46,307] [INFO] Selected 19 target genomes.
[2023-06-30 11:38:46,307] [INFO] Target genome list was writen to GCA_025347245.1_ASM2534724v1_genomic.fna/target_genomes.txt
[2023-06-30 11:38:46,308] [INFO] Task started: fastANI
[2023-06-30 11:38:46,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d557184-770b-48c1-abaa-8f4a2ca583a4/GCA_025347245.1_ASM2534724v1_genomic.fna.gz --refList GCA_025347245.1_ASM2534724v1_genomic.fna/target_genomes.txt --output GCA_025347245.1_ASM2534724v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 11:38:52,665] [INFO] Task succeeded: fastANI
[2023-06-30 11:38:52,665] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg86a58dca-c995-416f-94f5-7de2ec353dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 11:38:52,666] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg86a58dca-c995-416f-94f5-7de2ec353dad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 11:38:52,673] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2023-06-30 11:38:52,673] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-30 11:38:52,673] [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	98.5291	267	291	95	conclusive
Lactobacillus iners	strain=DSM 13335	GCA_000160875.1	147802	147802	type	True	98.5094	271	291	95	conclusive
Lactobacillus hominis	strain=DSM 23910	GCA_001436125.1	1203033	1203033	type	True	77.6422	66	291	95	below_threshold
Lactobacillus hominis	strain=type strain:CRBIP 24.179	GCA_000296835.1	1203033	1203033	type	True	77.5887	68	291	95	below_threshold
Lactobacillus gallinarum	strain=DSM 10532	GCA_001434975.1	52242	52242	type	True	77.2842	55	291	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 11:38:52,675] [INFO] DFAST Taxonomy check result was written to GCA_025347245.1_ASM2534724v1_genomic.fna/tc_result.tsv
[2023-06-30 11:38:52,676] [INFO] ===== Taxonomy check completed =====
[2023-06-30 11:38:52,676] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 11:38:52,676] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg86a58dca-c995-416f-94f5-7de2ec353dad/dqc_reference/checkm_data
[2023-06-30 11:38:52,677] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 11:38:52,691] [INFO] Task started: CheckM
[2023-06-30 11:38:52,692] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_025347245.1_ASM2534724v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_025347245.1_ASM2534724v1_genomic.fna/checkm_input GCA_025347245.1_ASM2534724v1_genomic.fna/checkm_result
[2023-06-30 11:39:05,590] [INFO] Task succeeded: CheckM
[2023-06-30 11:39:05,591] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 94.79%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-30 11:39:05,608] [INFO] ===== Completeness check finished =====
[2023-06-30 11:39:05,608] [INFO] ===== Start GTDB Search =====
[2023-06-30 11:39:05,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_025347245.1_ASM2534724v1_genomic.fna/markers.fasta)
[2023-06-30 11:39:05,609] [INFO] Task started: Blastn
[2023-06-30 11:39:05,609] [INFO] Running command: blastn -query GCA_025347245.1_ASM2534724v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg86a58dca-c995-416f-94f5-7de2ec353dad/dqc_reference/reference_markers_gtdb.fasta -out GCA_025347245.1_ASM2534724v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 11:39:06,386] [INFO] Task succeeded: Blastn
[2023-06-30 11:39:06,390] [INFO] Selected 23 target genomes.
[2023-06-30 11:39:06,390] [INFO] Target genome list was writen to GCA_025347245.1_ASM2534724v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 11:39:06,391] [INFO] Task started: fastANI
[2023-06-30 11:39:06,391] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d557184-770b-48c1-abaa-8f4a2ca583a4/GCA_025347245.1_ASM2534724v1_genomic.fna.gz --refList GCA_025347245.1_ASM2534724v1_genomic.fna/target_genomes_gtdb.txt --output GCA_025347245.1_ASM2534724v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 11:39:12,694] [INFO] Task succeeded: fastANI
[2023-06-30 11:39:12,700] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 11:39:12,700] [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	98.5094	271	291	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_017874575.1	s__Lactobacillus colini	78.2329	53	291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000296835.1	s__Lactobacillus hominis	77.5887	68	291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_001434975.1	s__Lactobacillus gallinarum	77.2842	55	291	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	77.1376	50	291	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.96	99.12	0.99	0.94	59	-
--------------------------------------------------------------------------------
[2023-06-30 11:39:12,702] [INFO] GTDB search result was written to GCA_025347245.1_ASM2534724v1_genomic.fna/result_gtdb.tsv
[2023-06-30 11:39:12,702] [INFO] ===== GTDB Search completed =====
[2023-06-30 11:39:12,705] [INFO] DFAST_QC result json was written to GCA_025347245.1_ASM2534724v1_genomic.fna/dqc_result.json
[2023-06-30 11:39:12,705] [INFO] DFAST_QC completed!
[2023-06-30 11:39:12,705] [INFO] Total running time: 0h0m30s