[2024-01-24 10:57:50,258] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:50,260] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:50,260] [INFO] DQC Reference Directory: /var/lib/cwl/stg1949e982-5f50-45dc-9f9b-19a792faf769/dqc_reference
[2024-01-24 10:57:52,642] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:52,643] [INFO] Task started: Prodigal
[2024-01-24 10:57:52,643] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa9d3918-e980-4974-9537-635e53dbfd54/GCF_013407595.1_ASM1340759v1_genomic.fna.gz | prodigal -d GCF_013407595.1_ASM1340759v1_genomic.fna/cds.fna -a GCF_013407595.1_ASM1340759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:00,876] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:00,877] [INFO] Task started: HMMsearch
[2024-01-24 10:58:00,877] [INFO] Running command: hmmsearch --tblout GCF_013407595.1_ASM1340759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1949e982-5f50-45dc-9f9b-19a792faf769/dqc_reference/reference_markers.hmm GCF_013407595.1_ASM1340759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:01,124] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:01,126] [INFO] Found 6/6 markers.
[2024-01-24 10:58:01,153] [INFO] Query marker FASTA was written to GCF_013407595.1_ASM1340759v1_genomic.fna/markers.fasta
[2024-01-24 10:58:01,154] [INFO] Task started: Blastn
[2024-01-24 10:58:01,154] [INFO] Running command: blastn -query GCF_013407595.1_ASM1340759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1949e982-5f50-45dc-9f9b-19a792faf769/dqc_reference/reference_markers.fasta -out GCF_013407595.1_ASM1340759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:01,776] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:01,780] [INFO] Selected 17 target genomes.
[2024-01-24 10:58:01,781] [INFO] Target genome list was writen to GCF_013407595.1_ASM1340759v1_genomic.fna/target_genomes.txt
[2024-01-24 10:58:01,818] [INFO] Task started: fastANI
[2024-01-24 10:58:01,818] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa9d3918-e980-4974-9537-635e53dbfd54/GCF_013407595.1_ASM1340759v1_genomic.fna.gz --refList GCF_013407595.1_ASM1340759v1_genomic.fna/target_genomes.txt --output GCF_013407595.1_ASM1340759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:09,913] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:09,914] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1949e982-5f50-45dc-9f9b-19a792faf769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:09,914] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1949e982-5f50-45dc-9f9b-19a792faf769/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:09,926] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 10:58:09,926] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:09,926] [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 absianus	strain=YH-lac23	GCA_013407595.1	2729623	2729623	type	True	99.9999	941	942	95	conclusive
Lacticaseibacillus daqingensis	strain=143-4(a)	GCA_003946115.1	2486014	2486014	type	True	80.7272	462	942	95	below_threshold
Lacticaseibacillus jixianensis	strain=159-4	GCA_003946485.1	2486012	2486012	type	True	78.1676	245	942	95	below_threshold
Lacticaseibacillus baoqingensis	strain=47-3	GCA_003946165.1	2486013	2486013	type	True	78.1337	100	942	95	below_threshold
Lacticaseibacillus camelliae	strain=DSM 22697	GCA_001436615.1	381742	381742	type	True	77.9514	189	942	95	below_threshold
Lacticaseibacillus camelliae	strain=JCM 13995	GCA_001311195.1	381742	381742	type	True	77.9174	177	942	95	below_threshold
Lacticaseibacillus hegangensis	strain=73-4	GCA_003946465.1	2486010	2486010	type	True	77.7189	195	942	95	below_threshold
Lacticaseibacillus saniviri	strain=DSM 24301	GCA_001437465.1	931533	931533	type	True	77.0163	58	942	95	below_threshold
Lacticaseibacillus saniviri	strain=JCM 17471	GCA_001311785.1	931533	931533	type	True	76.9293	57	942	95	below_threshold
Schleiferilactobacillus shenzhenensis	strain=LY-73	GCA_000469325.1	1231337	1231337	type	True	75.9007	67	942	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:09,929] [INFO] DFAST Taxonomy check result was written to GCF_013407595.1_ASM1340759v1_genomic.fna/tc_result.tsv
[2024-01-24 10:58:09,929] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:09,929] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:09,930] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1949e982-5f50-45dc-9f9b-19a792faf769/dqc_reference/checkm_data
[2024-01-24 10:58:09,931] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:09,960] [INFO] Task started: CheckM
[2024-01-24 10:58:09,960] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013407595.1_ASM1340759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013407595.1_ASM1340759v1_genomic.fna/checkm_input GCF_013407595.1_ASM1340759v1_genomic.fna/checkm_result
[2024-01-24 10:58:38,859] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:38,861] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.48%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:38,886] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:38,887] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:38,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013407595.1_ASM1340759v1_genomic.fna/markers.fasta)
[2024-01-24 10:58:38,888] [INFO] Task started: Blastn
[2024-01-24 10:58:38,888] [INFO] Running command: blastn -query GCF_013407595.1_ASM1340759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1949e982-5f50-45dc-9f9b-19a792faf769/dqc_reference/reference_markers_gtdb.fasta -out GCF_013407595.1_ASM1340759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:39,733] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:39,736] [INFO] Selected 14 target genomes.
[2024-01-24 10:58:39,737] [INFO] Target genome list was writen to GCF_013407595.1_ASM1340759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:39,747] [INFO] Task started: fastANI
[2024-01-24 10:58:39,748] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa9d3918-e980-4974-9537-635e53dbfd54/GCF_013407595.1_ASM1340759v1_genomic.fna.gz --refList GCF_013407595.1_ASM1340759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013407595.1_ASM1340759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:46,534] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:46,545] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:46,545] [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_013407595.1	s__Lacticaseibacillus absianus	99.9999	941	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003946115.1	s__Lacticaseibacillus daqingensis	80.7494	460	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946175.1	s__Lacticaseibacillus suibinensis	78.7115	115	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.05	98.05	0.90	0.90	2	-
GCF_016861845.1	s__Lacticaseibacillus sp900540605	78.3232	128	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.61	99.51	0.94	0.94	3	-
GCF_003946485.1	s__Lacticaseibacillus jixianensis	78.1531	246	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946165.1	s__Lacticaseibacillus baoqingensis	78.1337	100	942	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	77.9238	176	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	1.00	1.00	2	-
GCF_003946465.1	s__Lacticaseibacillus hegangensis	77.7353	194	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
GCF_001311785.1	s__Lacticaseibacillus saniviri	76.9293	57	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.88	99.88	0.99	0.99	3	-
GCF_000469325.1	s__Schleiferilactobacillus shenzhenensis	75.9007	67	942	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Schleiferilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:46,547] [INFO] GTDB search result was written to GCF_013407595.1_ASM1340759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:46,548] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:46,551] [INFO] DFAST_QC result json was written to GCF_013407595.1_ASM1340759v1_genomic.fna/dqc_result.json
[2024-01-24 10:58:46,551] [INFO] DFAST_QC completed!
[2024-01-24 10:58:46,551] [INFO] Total running time: 0h0m56s