[2024-01-24 12:46:35,255] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:46:35,257] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:46:35,257] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3c5d164-cd45-4c40-8ba7-10318eda8af2/dqc_reference
[2024-01-24 12:46:36,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:46:36,412] [INFO] Task started: Prodigal
[2024-01-24 12:46:36,412] [INFO] Running command: gunzip -c /var/lib/cwl/stg10b8cd28-6669-45e6-b98d-749b815a781d/GCF_025490915.1_ASM2549091v1_genomic.fna.gz | prodigal -d GCF_025490915.1_ASM2549091v1_genomic.fna/cds.fna -a GCF_025490915.1_ASM2549091v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:46:44,539] [INFO] Task succeeded: Prodigal
[2024-01-24 12:46:44,540] [INFO] Task started: HMMsearch
[2024-01-24 12:46:44,540] [INFO] Running command: hmmsearch --tblout GCF_025490915.1_ASM2549091v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3c5d164-cd45-4c40-8ba7-10318eda8af2/dqc_reference/reference_markers.hmm GCF_025490915.1_ASM2549091v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:46:44,719] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:46:44,720] [INFO] Found 6/6 markers.
[2024-01-24 12:46:44,745] [INFO] Query marker FASTA was written to GCF_025490915.1_ASM2549091v1_genomic.fna/markers.fasta
[2024-01-24 12:46:44,745] [INFO] Task started: Blastn
[2024-01-24 12:46:44,745] [INFO] Running command: blastn -query GCF_025490915.1_ASM2549091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c5d164-cd45-4c40-8ba7-10318eda8af2/dqc_reference/reference_markers.fasta -out GCF_025490915.1_ASM2549091v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:46:45,308] [INFO] Task succeeded: Blastn
[2024-01-24 12:46:45,311] [INFO] Selected 24 target genomes.
[2024-01-24 12:46:45,312] [INFO] Target genome list was writen to GCF_025490915.1_ASM2549091v1_genomic.fna/target_genomes.txt
[2024-01-24 12:46:45,352] [INFO] Task started: fastANI
[2024-01-24 12:46:45,353] [INFO] Running command: fastANI --query /var/lib/cwl/stg10b8cd28-6669-45e6-b98d-749b815a781d/GCF_025490915.1_ASM2549091v1_genomic.fna.gz --refList GCF_025490915.1_ASM2549091v1_genomic.fna/target_genomes.txt --output GCF_025490915.1_ASM2549091v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:46:58,254] [INFO] Task succeeded: fastANI
[2024-01-24 12:46:58,254] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3c5d164-cd45-4c40-8ba7-10318eda8af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:46:58,255] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3c5d164-cd45-4c40-8ba7-10318eda8af2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:46:58,266] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:46:58,266] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:46:58,266] [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 daqingensis	strain=143-4(a)	GCA_003946115.1	2486014	2486014	type	True	80.5098	382	920	95	below_threshold
Lacticaseibacillus absianus	strain=YH-lac23	GCA_013407595.1	2729623	2729623	type	True	80.0733	366	920	95	below_threshold
Lacticaseibacillus hegangensis	strain=73-4	GCA_003946465.1	2486010	2486010	type	True	78.6692	254	920	95	below_threshold
Lacticaseibacillus jixianensis	strain=159-4	GCA_003946485.1	2486012	2486012	type	True	78.3249	277	920	95	below_threshold
Lacticaseibacillus camelliae	strain=JCM 13995	GCA_001311195.1	381742	381742	type	True	78.2021	218	920	95	below_threshold
Lacticaseibacillus suilingensis	strain=ZW152	GCA_016861845.1	2799577	2799577	type	True	78.0725	180	920	95	below_threshold
Lacticaseibacillus camelliae	strain=DSM 22697	GCA_001436615.1	381742	381742	type	True	78.0364	238	920	95	below_threshold
Lacticaseibacillus manihotivorans	strain=JCM 12514	GCA_001311155.1	88233	88233	type	True	77.9706	82	920	95	below_threshold
Lacticaseibacillus yichunensis	strain=33-1	GCA_003946405.1	2486015	2486015	type	True	77.8805	213	920	95	below_threshold
Lacticaseibacillus nasuensis	strain=JCM 17158	GCA_001311255.1	944671	944671	type	True	77.8773	209	920	95	below_threshold
Lacticaseibacillus nasuensis	strain=JCM 17158	GCA_001434705.1	944671	944671	type	True	77.8023	229	920	95	below_threshold
Lacticaseibacillus suibinensis	strain=247-3	GCA_003946175.1	2486011	2486011	type	True	77.5346	175	920	95	below_threshold
Lacticaseibacillus sharpeae	strain=JCM 1186	GCA_001311055.1	1626	1626	type	True	77.3954	94	920	95	below_threshold
Levilactobacillus spicheri	strain=DSM 15429	GCA_001435095.1	216463	216463	type	True	75.7181	51	920	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:46:58,268] [INFO] DFAST Taxonomy check result was written to GCF_025490915.1_ASM2549091v1_genomic.fna/tc_result.tsv
[2024-01-24 12:46:58,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:46:58,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:46:58,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3c5d164-cd45-4c40-8ba7-10318eda8af2/dqc_reference/checkm_data
[2024-01-24 12:46:58,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:46:58,298] [INFO] Task started: CheckM
[2024-01-24 12:46:58,298] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025490915.1_ASM2549091v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025490915.1_ASM2549091v1_genomic.fna/checkm_input GCF_025490915.1_ASM2549091v1_genomic.fna/checkm_result
[2024-01-24 12:47:26,605] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:26,606] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:26,627] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:26,627] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:26,628] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025490915.1_ASM2549091v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:26,628] [INFO] Task started: Blastn
[2024-01-24 12:47:26,628] [INFO] Running command: blastn -query GCF_025490915.1_ASM2549091v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3c5d164-cd45-4c40-8ba7-10318eda8af2/dqc_reference/reference_markers_gtdb.fasta -out GCF_025490915.1_ASM2549091v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:27,449] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:27,453] [INFO] Selected 18 target genomes.
[2024-01-24 12:47:27,453] [INFO] Target genome list was writen to GCF_025490915.1_ASM2549091v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:27,475] [INFO] Task started: fastANI
[2024-01-24 12:47:27,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg10b8cd28-6669-45e6-b98d-749b815a781d/GCF_025490915.1_ASM2549091v1_genomic.fna.gz --refList GCF_025490915.1_ASM2549091v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025490915.1_ASM2549091v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:38,072] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:38,082] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:47:38,082] [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_003946115.1	s__Lacticaseibacillus daqingensis	80.4912	383	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013407595.1	s__Lacticaseibacillus absianus	80.0486	368	920	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	78.6855	252	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	95.70	95.61	0.83	0.83	3	-
GCF_003946165.1	s__Lacticaseibacillus baoqingensis	78.6035	99	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946485.1	s__Lacticaseibacillus jixianensis	78.3179	277	920	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	78.2182	217	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.89	99.89	1.00	1.00	2	-
GCF_016861845.1	s__Lacticaseibacillus sp900540605	78.0731	180	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.61	99.51	0.94	0.94	3	-
GCF_003946405.1	s__Lacticaseibacillus yichunensis	77.8805	213	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434705.1	s__Lacticaseibacillus nasuensis	77.8023	229	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.88	99.88	1.00	1.00	2	-
GCF_003946175.1	s__Lacticaseibacillus suibinensis	77.5168	176	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.05	98.05	0.90	0.90	2	-
GCF_001436225.1	s__Lacticaseibacillus sharpeae	77.4076	97	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.95	99.95	0.98	0.98	2	-
GCF_009687905.1	s__Lacticaseibacillus zhaodongensis	77.1855	80	920	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:38,085] [INFO] GTDB search result was written to GCF_025490915.1_ASM2549091v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:38,085] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:38,090] [INFO] DFAST_QC result json was written to GCF_025490915.1_ASM2549091v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:38,090] [INFO] DFAST_QC completed!
[2024-01-24 12:47:38,090] [INFO] Total running time: 0h1m3s