[2024-01-25 18:06:05,472] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:06:05,475] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:06:05,475] [INFO] DQC Reference Directory: /var/lib/cwl/stg08cac71f-a7f3-4d17-a4ec-33aef7e8187b/dqc_reference
[2024-01-25 18:06:06,621] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:06:06,622] [INFO] Task started: Prodigal
[2024-01-25 18:06:06,622] [INFO] Running command: gunzip -c /var/lib/cwl/stg1cf17ffc-3dea-4f8a-b3fd-066e821d0ec9/GCF_001311175.1_ASM131117v1_genomic.fna.gz | prodigal -d GCF_001311175.1_ASM131117v1_genomic.fna/cds.fna -a GCF_001311175.1_ASM131117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:06:12,663] [INFO] Task succeeded: Prodigal
[2024-01-25 18:06:12,663] [INFO] Task started: HMMsearch
[2024-01-25 18:06:12,663] [INFO] Running command: hmmsearch --tblout GCF_001311175.1_ASM131117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg08cac71f-a7f3-4d17-a4ec-33aef7e8187b/dqc_reference/reference_markers.hmm GCF_001311175.1_ASM131117v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:06:12,841] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:06:12,842] [INFO] Found 6/6 markers.
[2024-01-25 18:06:12,864] [INFO] Query marker FASTA was written to GCF_001311175.1_ASM131117v1_genomic.fna/markers.fasta
[2024-01-25 18:06:12,865] [INFO] Task started: Blastn
[2024-01-25 18:06:12,865] [INFO] Running command: blastn -query GCF_001311175.1_ASM131117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cac71f-a7f3-4d17-a4ec-33aef7e8187b/dqc_reference/reference_markers.fasta -out GCF_001311175.1_ASM131117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:13,442] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:13,445] [INFO] Selected 13 target genomes.
[2024-01-25 18:06:13,445] [INFO] Target genome list was writen to GCF_001311175.1_ASM131117v1_genomic.fna/target_genomes.txt
[2024-01-25 18:06:13,458] [INFO] Task started: fastANI
[2024-01-25 18:06:13,458] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cf17ffc-3dea-4f8a-b3fd-066e821d0ec9/GCF_001311175.1_ASM131117v1_genomic.fna.gz --refList GCF_001311175.1_ASM131117v1_genomic.fna/target_genomes.txt --output GCF_001311175.1_ASM131117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:06:20,499] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:20,500] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg08cac71f-a7f3-4d17-a4ec-33aef7e8187b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:06:20,500] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg08cac71f-a7f3-4d17-a4ec-33aef7e8187b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:06:20,513] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:06:20,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:06:20,513] [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
Lacticaseibacillus pantheris	strain=JCM 12539	GCA_001311175.1	171523	171523	type	True	100.0	805	808	95	conclusive
Lacticaseibacillus pantheris	strain=DSM 15945	GCA_001435155.1	171523	171523	type	True	99.885	797	808	95	conclusive
Lacticaseibacillus pantheris	strain=NBRC 106106	GCA_001591865.1	171523	171523	type	True	99.749	710	808	95	conclusive
Lacticaseibacillus thailandensis	strain=JCM 13996	GCA_001312865.1	381741	381741	type	True	80.4903	370	808	95	below_threshold
Lacticaseibacillus thailandensis	strain=DSM 22698	GCA_001436135.1	381741	381741	type	True	80.4523	369	808	95	below_threshold
Lacticaseibacillus sharpeae	strain=JCM 1186	GCA_001311055.1	1626	1626	type	True	77.9344	98	808	95	below_threshold
Lacticaseibacillus sharpeae	strain=DSM 20505	GCA_001436225.1	1626	1626	type	True	77.8854	100	808	95	below_threshold
Lacticaseibacillus zhaodongensis	strain=1206-1	GCA_009687905.1	2668065	2668065	type	True	77.5169	92	808	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:06:20,517] [INFO] DFAST Taxonomy check result was written to GCF_001311175.1_ASM131117v1_genomic.fna/tc_result.tsv
[2024-01-25 18:06:20,519] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:06:20,519] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:06:20,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg08cac71f-a7f3-4d17-a4ec-33aef7e8187b/dqc_reference/checkm_data
[2024-01-25 18:06:20,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:06:20,555] [INFO] Task started: CheckM
[2024-01-25 18:06:20,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001311175.1_ASM131117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001311175.1_ASM131117v1_genomic.fna/checkm_input GCF_001311175.1_ASM131117v1_genomic.fna/checkm_result
[2024-01-25 18:06:43,224] [INFO] Task succeeded: CheckM
[2024-01-25 18:06:43,225] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:06:43,252] [INFO] ===== Completeness check finished =====
[2024-01-25 18:06:43,252] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:06:43,252] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001311175.1_ASM131117v1_genomic.fna/markers.fasta)
[2024-01-25 18:06:43,253] [INFO] Task started: Blastn
[2024-01-25 18:06:43,253] [INFO] Running command: blastn -query GCF_001311175.1_ASM131117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg08cac71f-a7f3-4d17-a4ec-33aef7e8187b/dqc_reference/reference_markers_gtdb.fasta -out GCF_001311175.1_ASM131117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:06:44,204] [INFO] Task succeeded: Blastn
[2024-01-25 18:06:44,208] [INFO] Selected 22 target genomes.
[2024-01-25 18:06:44,208] [INFO] Target genome list was writen to GCF_001311175.1_ASM131117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:06:44,245] [INFO] Task started: fastANI
[2024-01-25 18:06:44,245] [INFO] Running command: fastANI --query /var/lib/cwl/stg1cf17ffc-3dea-4f8a-b3fd-066e821d0ec9/GCF_001311175.1_ASM131117v1_genomic.fna.gz --refList GCF_001311175.1_ASM131117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001311175.1_ASM131117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:06:55,845] [INFO] Task succeeded: fastANI
[2024-01-25 18:06:55,851] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:06:55,851] [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_001311175.1	s__Lacticaseibacillus pantheris	100.0	805	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	0.99	0.98	3	conclusive
GCF_001312865.1	s__Lacticaseibacillus thailandensis	80.4805	371	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	0.99	0.99	2	-
GCF_004010095.1	s__Lacticaseibacillus hulanensis	78.3024	105	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001311195.1	s__Lacticaseibacillus camelliae	78.0396	55	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	1.00	1.00	2	-
GCF_001436225.1	s__Lacticaseibacillus sharpeae	77.8854	100	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_003946025.1	s__Lacticaseibacillus songhuajiangensis	77.7351	99	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946465.1	s__Lacticaseibacillus hegangensis	77.7151	52	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
GCF_009687905.1	s__Lacticaseibacillus zhaodongensis	77.5169	92	808	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:06:55,853] [INFO] GTDB search result was written to GCF_001311175.1_ASM131117v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:06:55,853] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:06:55,860] [INFO] DFAST_QC result json was written to GCF_001311175.1_ASM131117v1_genomic.fna/dqc_result.json
[2024-01-25 18:06:55,860] [INFO] DFAST_QC completed!
[2024-01-25 18:06:55,860] [INFO] Total running time: 0h0m50s