[2024-01-24 13:46:18,695] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:18,697] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:18,697] [INFO] DQC Reference Directory: /var/lib/cwl/stg4b74f880-2a2f-4c92-8a6a-483df0b5be75/dqc_reference
[2024-01-24 13:46:20,060] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:20,061] [INFO] Task started: Prodigal
[2024-01-24 13:46:20,062] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d46bf86-b1bc-4418-b16e-5fc461afec9f/GCF_007115095.1_ASM711509v1_genomic.fna.gz | prodigal -d GCF_007115095.1_ASM711509v1_genomic.fna/cds.fna -a GCF_007115095.1_ASM711509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:27,885] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:27,885] [INFO] Task started: HMMsearch
[2024-01-24 13:46:27,885] [INFO] Running command: hmmsearch --tblout GCF_007115095.1_ASM711509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4b74f880-2a2f-4c92-8a6a-483df0b5be75/dqc_reference/reference_markers.hmm GCF_007115095.1_ASM711509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:28,212] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:28,213] [INFO] Found 6/6 markers.
[2024-01-24 13:46:28,246] [INFO] Query marker FASTA was written to GCF_007115095.1_ASM711509v1_genomic.fna/markers.fasta
[2024-01-24 13:46:28,247] [INFO] Task started: Blastn
[2024-01-24 13:46:28,247] [INFO] Running command: blastn -query GCF_007115095.1_ASM711509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b74f880-2a2f-4c92-8a6a-483df0b5be75/dqc_reference/reference_markers.fasta -out GCF_007115095.1_ASM711509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:28,946] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:28,949] [INFO] Selected 14 target genomes.
[2024-01-24 13:46:28,949] [INFO] Target genome list was writen to GCF_007115095.1_ASM711509v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:28,956] [INFO] Task started: fastANI
[2024-01-24 13:46:28,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d46bf86-b1bc-4418-b16e-5fc461afec9f/GCF_007115095.1_ASM711509v1_genomic.fna.gz --refList GCF_007115095.1_ASM711509v1_genomic.fna/target_genomes.txt --output GCF_007115095.1_ASM711509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:38,294] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:38,295] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4b74f880-2a2f-4c92-8a6a-483df0b5be75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:38,295] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4b74f880-2a2f-4c92-8a6a-483df0b5be75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:38,307] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:38,308] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:38,308] [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 enshiensis	strain=HBUAS57009	GCA_007115095.1	2590213	2590213	type	True	100.0	997	997	95	conclusive
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	87.5182	766	997	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	86.9512	727	997	95	below_threshold
Levilactobacillus fujinensis	strain=218-6	GCA_003946335.1	2486024	2486024	type	True	85.5973	725	997	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	81.5767	462	997	95	below_threshold
Levilactobacillus angrenensis	strain=M1530-1	GCA_003946085.1	2486020	2486020	type	True	81.4524	447	997	95	below_threshold
Levilactobacillus cerevisiae	strain=DSM 100836	GCA_003946245.1	1704076	1704076	type	True	81.416	450	997	95	below_threshold
Levilactobacillus fuyuanensis	strain=244-4	GCA_003946395.1	2486022	2486022	type	True	81.2692	404	997	95	below_threshold
Levilactobacillus tongjiangensis	strain=218-10	GCA_003946345.1	2486023	2486023	type	True	81.2012	407	997	95	below_threshold
Levilactobacillus suantsaiihabitans	strain=BCRC 81129	GCA_004745505.1	2487722	2487722	type	True	80.8893	452	997	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	79.3046	80	997	95	below_threshold
Secundilactobacillus silagei	strain=DSM 27022	GCA_004354595.1	1293415	1293415	type	True	78.222	82	997	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	78.1373	79	997	95	below_threshold
Secundilactobacillus silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	77.9369	82	997	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:38,309] [INFO] DFAST Taxonomy check result was written to GCF_007115095.1_ASM711509v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:38,310] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:38,310] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:38,310] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4b74f880-2a2f-4c92-8a6a-483df0b5be75/dqc_reference/checkm_data
[2024-01-24 13:46:38,312] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:38,345] [INFO] Task started: CheckM
[2024-01-24 13:46:38,345] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007115095.1_ASM711509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007115095.1_ASM711509v1_genomic.fna/checkm_input GCF_007115095.1_ASM711509v1_genomic.fna/checkm_result
[2024-01-24 13:47:08,241] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:08,243] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:08,263] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:08,264] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:08,264] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007115095.1_ASM711509v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:08,264] [INFO] Task started: Blastn
[2024-01-24 13:47:08,265] [INFO] Running command: blastn -query GCF_007115095.1_ASM711509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4b74f880-2a2f-4c92-8a6a-483df0b5be75/dqc_reference/reference_markers_gtdb.fasta -out GCF_007115095.1_ASM711509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:09,093] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:09,097] [INFO] Selected 11 target genomes.
[2024-01-24 13:47:09,097] [INFO] Target genome list was writen to GCF_007115095.1_ASM711509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:09,123] [INFO] Task started: fastANI
[2024-01-24 13:47:09,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d46bf86-b1bc-4418-b16e-5fc461afec9f/GCF_007115095.1_ASM711509v1_genomic.fna.gz --refList GCF_007115095.1_ASM711509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007115095.1_ASM711509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:17,146] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:17,163] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:17,163] [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_007115095.1	s__Levilactobacillus enshiensis	100.0	997	997	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_016861695.1	s__Levilactobacillus sp016861695	87.5139	765	997	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	86.9483	727	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
GCF_003946335.1	s__Levilactobacillus fujinensis	85.5903	725	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861655.1	s__Levilactobacillus sp016861655	81.5767	462	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_003946085.1	s__Levilactobacillus angrenensis	81.4524	447	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946245.1	s__Levilactobacillus cerevisiae	81.416	450	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861585.1	s__Levilactobacillus sp016861585	81.3687	465	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_003946395.1	s__Levilactobacillus fuyuanensis	81.3122	402	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666485.1	s__Levilactobacillus brevis_A	81.2253	458	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	80.9033	451	997	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:17,165] [INFO] GTDB search result was written to GCF_007115095.1_ASM711509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:17,166] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:17,170] [INFO] DFAST_QC result json was written to GCF_007115095.1_ASM711509v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:17,170] [INFO] DFAST_QC completed!
[2024-01-24 13:47:17,170] [INFO] Total running time: 0h0m58s