[2024-01-24 13:13:03,063] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:13:03,065] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:13:03,065] [INFO] DQC Reference Directory: /var/lib/cwl/stg0d0f967e-15c9-4510-913d-fb1e29a7ec4e/dqc_reference
[2024-01-24 13:13:04,268] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:13:04,269] [INFO] Task started: Prodigal
[2024-01-24 13:13:04,269] [INFO] Running command: gunzip -c /var/lib/cwl/stg123f8c2f-6320-48bd-ae9f-a11560312677/GCF_014145555.1_ASM1414555v1_genomic.fna.gz | prodigal -d GCF_014145555.1_ASM1414555v1_genomic.fna/cds.fna -a GCF_014145555.1_ASM1414555v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:13:09,052] [INFO] Task succeeded: Prodigal
[2024-01-24 13:13:09,053] [INFO] Task started: HMMsearch
[2024-01-24 13:13:09,053] [INFO] Running command: hmmsearch --tblout GCF_014145555.1_ASM1414555v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0d0f967e-15c9-4510-913d-fb1e29a7ec4e/dqc_reference/reference_markers.hmm GCF_014145555.1_ASM1414555v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:13:09,292] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:13:09,293] [INFO] Found 6/6 markers.
[2024-01-24 13:13:09,319] [INFO] Query marker FASTA was written to GCF_014145555.1_ASM1414555v1_genomic.fna/markers.fasta
[2024-01-24 13:13:09,319] [INFO] Task started: Blastn
[2024-01-24 13:13:09,320] [INFO] Running command: blastn -query GCF_014145555.1_ASM1414555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0f967e-15c9-4510-913d-fb1e29a7ec4e/dqc_reference/reference_markers.fasta -out GCF_014145555.1_ASM1414555v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:09,884] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:09,888] [INFO] Selected 15 target genomes.
[2024-01-24 13:13:09,888] [INFO] Target genome list was writen to GCF_014145555.1_ASM1414555v1_genomic.fna/target_genomes.txt
[2024-01-24 13:13:10,039] [INFO] Task started: fastANI
[2024-01-24 13:13:10,039] [INFO] Running command: fastANI --query /var/lib/cwl/stg123f8c2f-6320-48bd-ae9f-a11560312677/GCF_014145555.1_ASM1414555v1_genomic.fna.gz --refList GCF_014145555.1_ASM1414555v1_genomic.fna/target_genomes.txt --output GCF_014145555.1_ASM1414555v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:13:16,583] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:16,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0d0f967e-15c9-4510-913d-fb1e29a7ec4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:13:16,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0d0f967e-15c9-4510-913d-fb1e29a7ec4e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:13:16,596] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:13:16,596] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:13:16,596] [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
Limosilactobacillus albertensis	strain=Lr3000	GCA_014145555.1	2759752	2759752	type	True	100.0	793	794	95	inconclusive
Limosilactobacillus caviae	strain=CCM 8609	GCA_014635905.1	1769424	1769424	type	True	95.3776	660	794	95	inconclusive
Limosilactobacillus balticus	strain=BG-AF3-A	GCA_014145615.1	2759747	2759747	type	True	83.4577	475	794	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_001434615.1	557436	1598	type	True	83.2765	408	794	95	below_threshold
Limosilactobacillus reuteri subsp. murium	strain=lpuph1	GCA_000179455.1	863368	1598	type	True	83.0944	421	794	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=JCM 1112	GCA_000010005.1	557436	1598	type	True	83.0841	445	794	95	below_threshold
Limosilactobacillus reuteri subsp. reuteri	strain=DSM 20016	GCA_000016825.1	557436	1598	type	True	83.069	441	794	95	below_threshold
Limosilactobacillus reuteri subsp. rodentium	strain=100-23	GCA_000168255.1	349123	1598	type	True	83.0256	496	794	95	below_threshold
Limosilactobacillus agrestis	strain=WF-MT5-A	GCA_014145585.1	2759748	2759748	type	True	82.4702	425	794	95	below_threshold
Limosilactobacillus rudii	strain=STM3_1	GCA_014145455.1	2759755	2759755	type	True	81.6712	449	794	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:13:16,597] [INFO] DFAST Taxonomy check result was written to GCF_014145555.1_ASM1414555v1_genomic.fna/tc_result.tsv
[2024-01-24 13:13:16,598] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:13:16,598] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:13:16,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0d0f967e-15c9-4510-913d-fb1e29a7ec4e/dqc_reference/checkm_data
[2024-01-24 13:13:16,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:13:16,623] [INFO] Task started: CheckM
[2024-01-24 13:13:16,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_014145555.1_ASM1414555v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_014145555.1_ASM1414555v1_genomic.fna/checkm_input GCF_014145555.1_ASM1414555v1_genomic.fna/checkm_result
[2024-01-24 13:13:38,158] [INFO] Task succeeded: CheckM
[2024-01-24 13:13:38,160] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:13:38,181] [INFO] ===== Completeness check finished =====
[2024-01-24 13:13:38,182] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:13:38,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_014145555.1_ASM1414555v1_genomic.fna/markers.fasta)
[2024-01-24 13:13:38,183] [INFO] Task started: Blastn
[2024-01-24 13:13:38,183] [INFO] Running command: blastn -query GCF_014145555.1_ASM1414555v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0d0f967e-15c9-4510-913d-fb1e29a7ec4e/dqc_reference/reference_markers_gtdb.fasta -out GCF_014145555.1_ASM1414555v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:13:39,001] [INFO] Task succeeded: Blastn
[2024-01-24 13:13:39,004] [INFO] Selected 8 target genomes.
[2024-01-24 13:13:39,005] [INFO] Target genome list was writen to GCF_014145555.1_ASM1414555v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:13:39,114] [INFO] Task started: fastANI
[2024-01-24 13:13:39,114] [INFO] Running command: fastANI --query /var/lib/cwl/stg123f8c2f-6320-48bd-ae9f-a11560312677/GCF_014145555.1_ASM1414555v1_genomic.fna.gz --refList GCF_014145555.1_ASM1414555v1_genomic.fna/target_genomes_gtdb.txt --output GCF_014145555.1_ASM1414555v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:13:42,854] [INFO] Task succeeded: fastANI
[2024-01-24 13:13:42,865] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:13:42,865] [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_014635905.1	s__Limosilactobacillus caviae	95.3776	660	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.34	95.38	0.89	0.84	7	conclusive
GCF_014145615.1	s__Limosilactobacillus balticus	83.4719	474	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.51	98.51	0.89	0.89	2	-
GCF_000016825.1	s__Limosilactobacillus reuteri	83.0433	442	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	96.73	95.25	0.84	0.75	135	-
GCF_013694365.1	s__Limosilactobacillus reuteri_E	83.0372	421	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	97.28	96.40	0.80	0.72	58	-
GCA_003072625.1	s__Limosilactobacillus reuteri_D	82.7218	426	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	95.43	95.30	0.77	0.72	32	-
GCF_009663775.1	s__Limosilactobacillus sp009663775	82.4942	447	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.62	98.62	0.83	0.83	2	-
GCF_014145585.1	s__Limosilactobacillus agrestis	82.4702	425	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	98.60	98.25	0.88	0.88	3	-
GCF_014145455.1	s__Limosilactobacillus rudii	81.6712	449	794	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Limosilactobacillus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:13:42,868] [INFO] GTDB search result was written to GCF_014145555.1_ASM1414555v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:13:42,869] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:13:42,872] [INFO] DFAST_QC result json was written to GCF_014145555.1_ASM1414555v1_genomic.fna/dqc_result.json
[2024-01-24 13:13:42,872] [INFO] DFAST_QC completed!
[2024-01-24 13:13:42,872] [INFO] Total running time: 0h0m40s