[2024-01-25 17:37:51,100] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:51,104] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:51,104] [INFO] DQC Reference Directory: /var/lib/cwl/stg3220efeb-5b64-4894-8e5c-ab98950e9da4/dqc_reference
[2024-01-25 17:37:52,254] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:52,254] [INFO] Task started: Prodigal
[2024-01-25 17:37:52,255] [INFO] Running command: gunzip -c /var/lib/cwl/stg7faec5a8-c4b7-49e0-8b5f-6ce537ce5e50/GCF_003946095.1_ASM394609v1_genomic.fna.gz | prodigal -d GCF_003946095.1_ASM394609v1_genomic.fna/cds.fna -a GCF_003946095.1_ASM394609v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:37:57,229] [INFO] Task succeeded: Prodigal
[2024-01-25 17:37:57,229] [INFO] Task started: HMMsearch
[2024-01-25 17:37:57,230] [INFO] Running command: hmmsearch --tblout GCF_003946095.1_ASM394609v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3220efeb-5b64-4894-8e5c-ab98950e9da4/dqc_reference/reference_markers.hmm GCF_003946095.1_ASM394609v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:37:57,436] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:37:57,437] [INFO] Found 6/6 markers.
[2024-01-25 17:37:57,459] [INFO] Query marker FASTA was written to GCF_003946095.1_ASM394609v1_genomic.fna/markers.fasta
[2024-01-25 17:37:57,460] [INFO] Task started: Blastn
[2024-01-25 17:37:57,460] [INFO] Running command: blastn -query GCF_003946095.1_ASM394609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3220efeb-5b64-4894-8e5c-ab98950e9da4/dqc_reference/reference_markers.fasta -out GCF_003946095.1_ASM394609v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:37:58,029] [INFO] Task succeeded: Blastn
[2024-01-25 17:37:58,031] [INFO] Selected 13 target genomes.
[2024-01-25 17:37:58,032] [INFO] Target genome list was writen to GCF_003946095.1_ASM394609v1_genomic.fna/target_genomes.txt
[2024-01-25 17:37:58,037] [INFO] Task started: fastANI
[2024-01-25 17:37:58,037] [INFO] Running command: fastANI --query /var/lib/cwl/stg7faec5a8-c4b7-49e0-8b5f-6ce537ce5e50/GCF_003946095.1_ASM394609v1_genomic.fna.gz --refList GCF_003946095.1_ASM394609v1_genomic.fna/target_genomes.txt --output GCF_003946095.1_ASM394609v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:05,708] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:05,709] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3220efeb-5b64-4894-8e5c-ab98950e9da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:05,709] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3220efeb-5b64-4894-8e5c-ab98950e9da4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:05,717] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:38:05,717] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:38:05,717] [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 lindianensis	strain=220-4	GCA_003946095.1	2486018	2486018	type	True	100.0	745	748	95	conclusive
Levilactobacillus paucivorans	strain=DSM 22467	GCA_001437125.1	616990	616990	type	True	90.8606	648	748	95	below_threshold
Levilactobacillus huananensis	strain=151-2B	GCA_003946145.1	2486019	2486019	type	True	87.1136	615	748	95	below_threshold
Levilactobacillus parabrevis	strain=ATCC 53295	GCA_001434055.1	357278	357278	type	True	81.0524	382	748	95	below_threshold
Levilactobacillus parabrevis	strain=LMG 11984	GCA_001437515.1	357278	357278	type	True	80.9886	387	748	95	below_threshold
Levilactobacillus hammesii	strain=DSM 16381	GCA_001434395.1	267633	267633	type	True	80.9868	356	748	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	80.7748	352	748	95	below_threshold
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	80.4016	333	748	95	below_threshold
Levilactobacillus enshiensis	strain=HBUAS57009	GCA_007115095.1	2590213	2590213	type	True	80.3782	332	748	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.9445	79	748	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:05,719] [INFO] DFAST Taxonomy check result was written to GCF_003946095.1_ASM394609v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:05,720] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:05,720] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:05,720] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3220efeb-5b64-4894-8e5c-ab98950e9da4/dqc_reference/checkm_data
[2024-01-25 17:38:05,721] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:05,747] [INFO] Task started: CheckM
[2024-01-25 17:38:05,747] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003946095.1_ASM394609v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003946095.1_ASM394609v1_genomic.fna/checkm_input GCF_003946095.1_ASM394609v1_genomic.fna/checkm_result
[2024-01-25 17:38:26,098] [INFO] Task succeeded: CheckM
[2024-01-25 17:38:26,099] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:38:26,117] [INFO] ===== Completeness check finished =====
[2024-01-25 17:38:26,117] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:38:26,118] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003946095.1_ASM394609v1_genomic.fna/markers.fasta)
[2024-01-25 17:38:26,118] [INFO] Task started: Blastn
[2024-01-25 17:38:26,118] [INFO] Running command: blastn -query GCF_003946095.1_ASM394609v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3220efeb-5b64-4894-8e5c-ab98950e9da4/dqc_reference/reference_markers_gtdb.fasta -out GCF_003946095.1_ASM394609v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:26,972] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:26,975] [INFO] Selected 10 target genomes.
[2024-01-25 17:38:26,976] [INFO] Target genome list was writen to GCF_003946095.1_ASM394609v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:38:26,981] [INFO] Task started: fastANI
[2024-01-25 17:38:26,981] [INFO] Running command: fastANI --query /var/lib/cwl/stg7faec5a8-c4b7-49e0-8b5f-6ce537ce5e50/GCF_003946095.1_ASM394609v1_genomic.fna.gz --refList GCF_003946095.1_ASM394609v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003946095.1_ASM394609v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:38:32,762] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:32,769] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:38:32,770] [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_003946095.1	s__Levilactobacillus lindianensis	100.0	744	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	90.8606	648	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_003946145.1	s__Levilactobacillus huananensis	87.1136	615	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	81.2532	401	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	81.0353	383	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	80.9876	356	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_016861695.1	s__Levilactobacillus sp016861695	80.7978	351	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_016861585.1	s__Levilactobacillus sp016861585	80.6169	363	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_016861655.1	s__Levilactobacillus sp016861655	80.523	345	748	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.63	95.63	0.89	0.89	2	-
GCF_012641095.1	s__Levilactobacillus sp012641095	80.4875	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	-
--------------------------------------------------------------------------------
[2024-01-25 17:38:32,771] [INFO] GTDB search result was written to GCF_003946095.1_ASM394609v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:38:32,771] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:38:32,774] [INFO] DFAST_QC result json was written to GCF_003946095.1_ASM394609v1_genomic.fna/dqc_result.json
[2024-01-25 17:38:32,774] [INFO] DFAST_QC completed!
[2024-01-25 17:38:32,774] [INFO] Total running time: 0h0m42s