[2024-01-24 14:05:36,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:36,646] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:36,646] [INFO] DQC Reference Directory: /var/lib/cwl/stga411ef73-73d1-4c3b-9390-0f1a6124ae5a/dqc_reference
[2024-01-24 14:05:38,072] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:38,073] [INFO] Task started: Prodigal
[2024-01-24 14:05:38,073] [INFO] Running command: gunzip -c /var/lib/cwl/stgf8c7f794-96f6-44d0-953d-f0530eeb9cda/GCF_005405425.1_ASM540542v1_genomic.fna.gz | prodigal -d GCF_005405425.1_ASM540542v1_genomic.fna/cds.fna -a GCF_005405425.1_ASM540542v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:44,469] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:44,470] [INFO] Task started: HMMsearch
[2024-01-24 14:05:44,470] [INFO] Running command: hmmsearch --tblout GCF_005405425.1_ASM540542v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga411ef73-73d1-4c3b-9390-0f1a6124ae5a/dqc_reference/reference_markers.hmm GCF_005405425.1_ASM540542v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:44,793] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:44,794] [INFO] Found 6/6 markers.
[2024-01-24 14:05:44,819] [INFO] Query marker FASTA was written to GCF_005405425.1_ASM540542v1_genomic.fna/markers.fasta
[2024-01-24 14:05:44,819] [INFO] Task started: Blastn
[2024-01-24 14:05:44,820] [INFO] Running command: blastn -query GCF_005405425.1_ASM540542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga411ef73-73d1-4c3b-9390-0f1a6124ae5a/dqc_reference/reference_markers.fasta -out GCF_005405425.1_ASM540542v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:45,458] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:45,462] [INFO] Selected 17 target genomes.
[2024-01-24 14:05:45,462] [INFO] Target genome list was writen to GCF_005405425.1_ASM540542v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:45,467] [INFO] Task started: fastANI
[2024-01-24 14:05:45,467] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8c7f794-96f6-44d0-953d-f0530eeb9cda/GCF_005405425.1_ASM540542v1_genomic.fna.gz --refList GCF_005405425.1_ASM540542v1_genomic.fna/target_genomes.txt --output GCF_005405425.1_ASM540542v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:56,602] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:56,603] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga411ef73-73d1-4c3b-9390-0f1a6124ae5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:56,603] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga411ef73-73d1-4c3b-9390-0f1a6124ae5a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:56,616] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:56,616] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:56,616] [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
Lactiplantibacillus modestisalitolerans	strain=NBRC 107235	GCA_005405425.1	1457219	1457219	type	True	100.0	896	897	95	conclusive
Lactiplantibacillus plajomi	strain=NBRC 107333	GCA_005405405.1	1457217	1457217	type	True	80.4313	401	897	95	below_threshold
Lactiplantibacillus garii	strain=FI11369	GCA_003885105.1	2306423	2306423	type	True	80.2486	402	897	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	80.1389	341	897	95	below_threshold
Lactiplantibacillus xiangfangensis	strain=LMG 26013	GCA_001438845.1	942150	942150	type	True	80.1378	348	897	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_003641165.1	271881	271881	type	True	80.0828	308	897	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	80.017	340	897	95	below_threshold
Lactiplantibacillus argentoratensis	strain=DSM 16365	GCA_001435215.1	271881	271881	type	True	79.9374	300	897	95	below_threshold
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	79.7437	313	897	95	below_threshold
Lactiplantibacillus dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	79.6678	261	897	95	below_threshold
Lactiplantibacillus herbarum	strain=TCF032-E4	GCA_001039045.1	1670446	1670446	type	True	79.5139	278	897	95	below_threshold
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	79.4768	307	897	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	77.3858	61	897	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:56,618] [INFO] DFAST Taxonomy check result was written to GCF_005405425.1_ASM540542v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:56,619] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:56,619] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:56,619] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga411ef73-73d1-4c3b-9390-0f1a6124ae5a/dqc_reference/checkm_data
[2024-01-24 14:05:56,621] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:56,650] [INFO] Task started: CheckM
[2024-01-24 14:05:56,650] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405425.1_ASM540542v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405425.1_ASM540542v1_genomic.fna/checkm_input GCF_005405425.1_ASM540542v1_genomic.fna/checkm_result
[2024-01-24 14:06:23,258] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:23,260] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:23,281] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:23,281] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:23,282] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405425.1_ASM540542v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:23,282] [INFO] Task started: Blastn
[2024-01-24 14:06:23,282] [INFO] Running command: blastn -query GCF_005405425.1_ASM540542v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga411ef73-73d1-4c3b-9390-0f1a6124ae5a/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405425.1_ASM540542v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:24,099] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:24,103] [INFO] Selected 14 target genomes.
[2024-01-24 14:06:24,103] [INFO] Target genome list was writen to GCF_005405425.1_ASM540542v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:24,112] [INFO] Task started: fastANI
[2024-01-24 14:06:24,113] [INFO] Running command: fastANI --query /var/lib/cwl/stgf8c7f794-96f6-44d0-953d-f0530eeb9cda/GCF_005405425.1_ASM540542v1_genomic.fna.gz --refList GCF_005405425.1_ASM540542v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405425.1_ASM540542v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:33,969] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:33,983] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:33,983] [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_005405425.1	s__Lactiplantibacillus modestisalitolerans	100.0	896	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005405405.1	s__Lactiplantibacillus plajomi	80.4106	403	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003885105.1	s__Lactiplantibacillus garii	80.2336	403	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003641185.1	s__Lactiplantibacillus pentosus	80.1389	341	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.89	96.07	0.90	0.86	56	-
GCF_001438845.1	s__Lactiplantibacillus xiangfangensis	80.1368	348	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	79.937	340	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_002970935.1	s__Lactiplantibacillus sp002970935	79.7622	240	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014131735.1	s__Lactiplantibacillus plantarum	79.7437	313	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	79.7355	251	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405105.1	s__Lactiplantibacillus dongliensis	79.6673	261	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001039045.1	s__Lactiplantibacillus herbarum	79.5139	278	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498955.2	s__Lactiplantibacillus fabifermentans	79.4604	308	897	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:33,985] [INFO] GTDB search result was written to GCF_005405425.1_ASM540542v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:33,986] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:33,991] [INFO] DFAST_QC result json was written to GCF_005405425.1_ASM540542v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:33,991] [INFO] DFAST_QC completed!
[2024-01-24 14:06:33,992] [INFO] Total running time: 0h0m57s