[2024-01-25 19:48:05,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:48:05,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:48:05,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a11b3f2-3913-46e9-9c01-b9b4dcf668ae/dqc_reference
[2024-01-25 19:48:06,678] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:48:06,679] [INFO] Task started: Prodigal
[2024-01-25 19:48:06,679] [INFO] Running command: gunzip -c /var/lib/cwl/stg8f1614ce-fd00-49bd-91a5-2184e3dc30b4/GCF_003946145.1_ASM394614v1_genomic.fna.gz | prodigal -d GCF_003946145.1_ASM394614v1_genomic.fna/cds.fna -a GCF_003946145.1_ASM394614v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:48:11,554] [INFO] Task succeeded: Prodigal
[2024-01-25 19:48:11,554] [INFO] Task started: HMMsearch
[2024-01-25 19:48:11,555] [INFO] Running command: hmmsearch --tblout GCF_003946145.1_ASM394614v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a11b3f2-3913-46e9-9c01-b9b4dcf668ae/dqc_reference/reference_markers.hmm GCF_003946145.1_ASM394614v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:48:11,761] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:48:11,763] [INFO] Found 6/6 markers.
[2024-01-25 19:48:11,786] [INFO] Query marker FASTA was written to GCF_003946145.1_ASM394614v1_genomic.fna/markers.fasta
[2024-01-25 19:48:11,787] [INFO] Task started: Blastn
[2024-01-25 19:48:11,787] [INFO] Running command: blastn -query GCF_003946145.1_ASM394614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a11b3f2-3913-46e9-9c01-b9b4dcf668ae/dqc_reference/reference_markers.fasta -out GCF_003946145.1_ASM394614v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:12,356] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:12,359] [INFO] Selected 15 target genomes.
[2024-01-25 19:48:12,359] [INFO] Target genome list was writen to GCF_003946145.1_ASM394614v1_genomic.fna/target_genomes.txt
[2024-01-25 19:48:12,374] [INFO] Task started: fastANI
[2024-01-25 19:48:12,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f1614ce-fd00-49bd-91a5-2184e3dc30b4/GCF_003946145.1_ASM394614v1_genomic.fna.gz --refList GCF_003946145.1_ASM394614v1_genomic.fna/target_genomes.txt --output GCF_003946145.1_ASM394614v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:48:20,762] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:20,763] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a11b3f2-3913-46e9-9c01-b9b4dcf668ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:48:20,763] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a11b3f2-3913-46e9-9c01-b9b4dcf668ae/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:48:20,770] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:48:20,770] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:48:20,770] [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
Levilactobacillus huananensis	strain=151-2B	GCA_003946145.1	2486019	2486019	type	True	100.0	748	748	95	conclusive
Levilactobacillus paucivorans	strain=DSM 22467	GCA_001437125.1	616990	616990	type	True	88.2225	606	748	95	below_threshold
Levilactobacillus lindianensis	strain=220-4	GCA_003946095.1	2486018	2486018	type	True	87.1779	596	748	95	below_threshold
Levilactobacillus parabrevis	strain=LMG 11984	GCA_001437515.1	357278	357278	type	True	81.2964	338	748	95	below_threshold
Levilactobacillus parabrevis	strain=ATCC 53295	GCA_001434055.1	357278	357278	type	True	81.2926	332	748	95	below_threshold
Levilactobacillus hammesii	strain=DSM 16381	GCA_001434395.1	267633	267633	type	True	81.0586	342	748	95	below_threshold
Levilactobacillus fuyuanensis	strain=244-4	GCA_003946395.1	2486022	2486022	type	True	80.7273	353	748	95	below_threshold
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	80.5795	297	748	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	80.432	321	748	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	80.2089	312	748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:48:20,772] [INFO] DFAST Taxonomy check result was written to GCF_003946145.1_ASM394614v1_genomic.fna/tc_result.tsv
[2024-01-25 19:48:20,773] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:48:20,773] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:48:20,773] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a11b3f2-3913-46e9-9c01-b9b4dcf668ae/dqc_reference/checkm_data
[2024-01-25 19:48:20,774] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:48:20,800] [INFO] Task started: CheckM
[2024-01-25 19:48:20,800] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003946145.1_ASM394614v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003946145.1_ASM394614v1_genomic.fna/checkm_input GCF_003946145.1_ASM394614v1_genomic.fna/checkm_result
[2024-01-25 19:48:40,867] [INFO] Task succeeded: CheckM
[2024-01-25 19:48:40,868] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:48:40,882] [INFO] ===== Completeness check finished =====
[2024-01-25 19:48:40,883] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:48:40,883] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003946145.1_ASM394614v1_genomic.fna/markers.fasta)
[2024-01-25 19:48:40,883] [INFO] Task started: Blastn
[2024-01-25 19:48:40,883] [INFO] Running command: blastn -query GCF_003946145.1_ASM394614v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a11b3f2-3913-46e9-9c01-b9b4dcf668ae/dqc_reference/reference_markers_gtdb.fasta -out GCF_003946145.1_ASM394614v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:48:41,655] [INFO] Task succeeded: Blastn
[2024-01-25 19:48:41,660] [INFO] Selected 11 target genomes.
[2024-01-25 19:48:41,661] [INFO] Target genome list was writen to GCF_003946145.1_ASM394614v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:48:41,676] [INFO] Task started: fastANI
[2024-01-25 19:48:41,676] [INFO] Running command: fastANI --query /var/lib/cwl/stg8f1614ce-fd00-49bd-91a5-2184e3dc30b4/GCF_003946145.1_ASM394614v1_genomic.fna.gz --refList GCF_003946145.1_ASM394614v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003946145.1_ASM394614v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:48:47,269] [INFO] Task succeeded: fastANI
[2024-01-25 19:48:47,276] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:48:47,276] [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_003946145.1	s__Levilactobacillus huananensis	100.0	748	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001437125.1	s__Levilactobacillus paucivorans	88.2178	607	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946095.1	s__Levilactobacillus lindianensis	87.1779	596	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434055.1	s__Levilactobacillus parabrevis	81.2926	332	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.99	99.98	0.99	0.98	3	-
GCF_001434395.1	s__Levilactobacillus hammesii	81.0426	341	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946395.1	s__Levilactobacillus fuyuanensis	80.7214	354	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641185.1	s__Levilactobacillus sp012641185	80.5683	298	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.99	95.94	0.88	0.87	3	-
GCF_016861695.1	s__Levilactobacillus sp016861695	80.4315	321	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641095.1	s__Levilactobacillus sp012641095	80.1981	332	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435525.1	s__Levilactobacillus koreensis	80.1905	313	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001433855.1	s__Levilactobacillus brevis	79.6126	234	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	97.91	96.65	0.91	0.84	85	-
--------------------------------------------------------------------------------
[2024-01-25 19:48:47,278] [INFO] GTDB search result was written to GCF_003946145.1_ASM394614v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:48:47,278] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:48:47,280] [INFO] DFAST_QC result json was written to GCF_003946145.1_ASM394614v1_genomic.fna/dqc_result.json
[2024-01-25 19:48:47,281] [INFO] DFAST_QC completed!
[2024-01-25 19:48:47,281] [INFO] Total running time: 0h0m42s