[2023-06-13 08:52:23,292] [INFO] DFAST_QC pipeline started.
[2023-06-13 08:52:23,295] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 08:52:23,295] [INFO] DQC Reference Directory: /var/lib/cwl/stgddb806fa-2c89-4e3c-844c-07b9747b0bb4/dqc_reference
[2023-06-13 08:52:24,576] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 08:52:24,577] [INFO] Task started: Prodigal
[2023-06-13 08:52:24,578] [INFO] Running command: gunzip -c /var/lib/cwl/stg6888be2f-78dd-4275-8a32-b8836644d214/GCA_022752655.1_ASM2275265v1_genomic.fna.gz | prodigal -d GCA_022752655.1_ASM2275265v1_genomic.fna/cds.fna -a GCA_022752655.1_ASM2275265v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 08:52:26,089] [INFO] Task succeeded: Prodigal
[2023-06-13 08:52:26,089] [INFO] Task started: HMMsearch
[2023-06-13 08:52:26,089] [INFO] Running command: hmmsearch --tblout GCA_022752655.1_ASM2275265v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddb806fa-2c89-4e3c-844c-07b9747b0bb4/dqc_reference/reference_markers.hmm GCA_022752655.1_ASM2275265v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 08:52:26,301] [INFO] Task succeeded: HMMsearch
[2023-06-13 08:52:26,302] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg6888be2f-78dd-4275-8a32-b8836644d214/GCA_022752655.1_ASM2275265v1_genomic.fna.gz]
[2023-06-13 08:52:26,315] [INFO] Query marker FASTA was written to GCA_022752655.1_ASM2275265v1_genomic.fna/markers.fasta
[2023-06-13 08:52:26,315] [INFO] Task started: Blastn
[2023-06-13 08:52:26,316] [INFO] Running command: blastn -query GCA_022752655.1_ASM2275265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddb806fa-2c89-4e3c-844c-07b9747b0bb4/dqc_reference/reference_markers.fasta -out GCA_022752655.1_ASM2275265v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:27,740] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:27,744] [INFO] Selected 5 target genomes.
[2023-06-13 08:52:27,745] [INFO] Target genome list was writen to GCA_022752655.1_ASM2275265v1_genomic.fna/target_genomes.txt
[2023-06-13 08:52:27,749] [INFO] Task started: fastANI
[2023-06-13 08:52:27,750] [INFO] Running command: fastANI --query /var/lib/cwl/stg6888be2f-78dd-4275-8a32-b8836644d214/GCA_022752655.1_ASM2275265v1_genomic.fna.gz --refList GCA_022752655.1_ASM2275265v1_genomic.fna/target_genomes.txt --output GCA_022752655.1_ASM2275265v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 08:52:29,056] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:29,057] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddb806fa-2c89-4e3c-844c-07b9747b0bb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 08:52:29,057] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddb806fa-2c89-4e3c-844c-07b9747b0bb4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 08:52:29,066] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2023-06-13 08:52:29,066] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-13 08:52:29,066] [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 mulieris	strain=c10Ua161M	GCA_007095465.1	2508708	2508708	type	True	99.8299	251	269	95	conclusive
Lactobacillus jensenii	strain=DSM 20557	GCA_001436455.1	109790	109790	type	True	88.6752	220	269	95	below_threshold
Lactobacillus jensenii	strain=ATCC 25258	GCA_018094625.1	109790	109790	type	True	88.5547	223	269	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_000425905.1	116089	116089	type	True	84.1774	178	269	95	below_threshold
Lactobacillus psittaci	strain=DSM 15354	GCA_001435695.1	116089	116089	type	True	84.1177	179	269	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 08:52:29,068] [INFO] DFAST Taxonomy check result was written to GCA_022752655.1_ASM2275265v1_genomic.fna/tc_result.tsv
[2023-06-13 08:52:29,069] [INFO] ===== Taxonomy check completed =====
[2023-06-13 08:52:29,069] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 08:52:29,069] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddb806fa-2c89-4e3c-844c-07b9747b0bb4/dqc_reference/checkm_data
[2023-06-13 08:52:29,070] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 08:52:29,085] [INFO] Task started: CheckM
[2023-06-13 08:52:29,085] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022752655.1_ASM2275265v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022752655.1_ASM2275265v1_genomic.fna/checkm_input GCA_022752655.1_ASM2275265v1_genomic.fna/checkm_result
[2023-06-13 08:52:43,640] [INFO] Task succeeded: CheckM
[2023-06-13 08:52:43,642] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 08:52:43,661] [INFO] ===== Completeness check finished =====
[2023-06-13 08:52:43,662] [INFO] ===== Start GTDB Search =====
[2023-06-13 08:52:43,662] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022752655.1_ASM2275265v1_genomic.fna/markers.fasta)
[2023-06-13 08:52:43,663] [INFO] Task started: Blastn
[2023-06-13 08:52:43,663] [INFO] Running command: blastn -query GCA_022752655.1_ASM2275265v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddb806fa-2c89-4e3c-844c-07b9747b0bb4/dqc_reference/reference_markers_gtdb.fasta -out GCA_022752655.1_ASM2275265v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 08:52:44,268] [INFO] Task succeeded: Blastn
[2023-06-13 08:52:44,272] [INFO] Selected 9 target genomes.
[2023-06-13 08:52:44,272] [INFO] Target genome list was writen to GCA_022752655.1_ASM2275265v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 08:52:44,307] [INFO] Task started: fastANI
[2023-06-13 08:52:44,308] [INFO] Running command: fastANI --query /var/lib/cwl/stg6888be2f-78dd-4275-8a32-b8836644d214/GCA_022752655.1_ASM2275265v1_genomic.fna.gz --refList GCA_022752655.1_ASM2275265v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022752655.1_ASM2275265v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 08:52:47,518] [INFO] Task succeeded: fastANI
[2023-06-13 08:52:47,528] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 08:52:47,528] [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_007095465.1	s__Lactobacillus mulieris	99.8299	251	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.54	96.91	0.92	0.85	18	conclusive
GCF_001436455.1	s__Lactobacillus jensenii	88.6752	220	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.86	99.75	0.93	0.88	31	-
GCF_000425905.1	s__Lactobacillus psittaci	84.1774	178	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.95	99.95	0.99	0.99	2	-
GCF_003423665.1	s__Lactobacillus rodentium	79.3241	65	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014803895.1	s__Lactobacillus sp014803895	78.8713	71	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004009905.1	s__Lactobacillus xujianguonis	78.6883	72	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.83	99.82	0.94	0.92	3	-
GCF_000296835.1	s__Lactobacillus hominis	78.5496	72	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.73	99.20	0.96	0.89	4	-
GCF_002916935.1	s__Lactobacillus panisapium	78.1748	57	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007570935.1	s__Lactobacillus sp007570935	78.0502	94	269	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 08:52:47,530] [INFO] GTDB search result was written to GCA_022752655.1_ASM2275265v1_genomic.fna/result_gtdb.tsv
[2023-06-13 08:52:47,531] [INFO] ===== GTDB Search completed =====
[2023-06-13 08:52:47,534] [INFO] DFAST_QC result json was written to GCA_022752655.1_ASM2275265v1_genomic.fna/dqc_result.json
[2023-06-13 08:52:47,535] [INFO] DFAST_QC completed!
[2023-06-13 08:52:47,535] [INFO] Total running time: 0h0m24s