[2024-01-24 14:28:15,956] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:28:15,958] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:28:15,958] [INFO] DQC Reference Directory: /var/lib/cwl/stg49f7ac91-b3ce-4119-a13c-2ced5a19281b/dqc_reference
[2024-01-24 14:28:17,938] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:28:17,939] [INFO] Task started: Prodigal
[2024-01-24 14:28:17,939] [INFO] Running command: gunzip -c /var/lib/cwl/stgb1377bd8-a492-49a0-b4a5-b11f3772df3d/GCF_019972835.1_ASM1997283v1_genomic.fna.gz | prodigal -d GCF_019972835.1_ASM1997283v1_genomic.fna/cds.fna -a GCF_019972835.1_ASM1997283v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:28:22,034] [INFO] Task succeeded: Prodigal
[2024-01-24 14:28:22,035] [INFO] Task started: HMMsearch
[2024-01-24 14:28:22,035] [INFO] Running command: hmmsearch --tblout GCF_019972835.1_ASM1997283v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49f7ac91-b3ce-4119-a13c-2ced5a19281b/dqc_reference/reference_markers.hmm GCF_019972835.1_ASM1997283v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:28:22,228] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:28:22,230] [INFO] Found 6/6 markers.
[2024-01-24 14:28:22,257] [INFO] Query marker FASTA was written to GCF_019972835.1_ASM1997283v1_genomic.fna/markers.fasta
[2024-01-24 14:28:22,257] [INFO] Task started: Blastn
[2024-01-24 14:28:22,257] [INFO] Running command: blastn -query GCF_019972835.1_ASM1997283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f7ac91-b3ce-4119-a13c-2ced5a19281b/dqc_reference/reference_markers.fasta -out GCF_019972835.1_ASM1997283v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:25,108] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:25,112] [INFO] Selected 21 target genomes.
[2024-01-24 14:28:25,112] [INFO] Target genome list was writen to GCF_019972835.1_ASM1997283v1_genomic.fna/target_genomes.txt
[2024-01-24 14:28:25,277] [INFO] Task started: fastANI
[2024-01-24 14:28:25,277] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1377bd8-a492-49a0-b4a5-b11f3772df3d/GCF_019972835.1_ASM1997283v1_genomic.fna.gz --refList GCF_019972835.1_ASM1997283v1_genomic.fna/target_genomes.txt --output GCF_019972835.1_ASM1997283v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:28:32,695] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:32,695] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49f7ac91-b3ce-4119-a13c-2ced5a19281b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:28:32,695] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49f7ac91-b3ce-4119-a13c-2ced5a19281b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:28:32,712] [INFO] Found 18 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:28:32,712] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:28:32,713] [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
Lactobacillus laiwuensis	strain=F551-2	GCA_019972835.1	2841034	2841034	type	True	100.0	660	662	95	conclusive
Lactobacillus huangpiensis	strain=F306-1	GCA_019972815.1	2799571	2799571	type	True	92.491	514	662	95	below_threshold
Lactobacillus apis	strain=CCM 8403	GCA_014635365.1	303541	303541	type	True	79.6491	240	662	95	below_threshold
Lactobacillus apis	strain=LMG 26964	GCA_002837055.1	303541	303541	type	True	79.5533	218	662	95	below_threshold
Lactobacillus bombicola	strain=R-53102	GCA_900112665.1	1505723	1505723	type	True	78.7828	191	662	95	below_threshold
Lactobacillus bombicola	strain=H70-3	GCA_002916915.1	1505723	1505723	type	True	78.778	188	662	95	below_threshold
Lactobacillus intestinalis	strain=DSM 6629	GCA_024397795.1	151781	151781	type	True	78.2289	105	662	95	below_threshold
Lactobacillus hamsteri	strain=DSM 5661	GCA_001434515.1	96565	96565	type	True	78.1201	111	662	95	below_threshold
Lactobacillus hamsteri	strain=JCM 6256	GCA_000615445.1	96565	96565	type	True	78.0013	114	662	95	below_threshold
Lactobacillus amylolyticus	strain=DSM 11664	GCA_001435665.1	83683	83683	type	True	77.8728	100	662	95	below_threshold
Lactobacillus kefiranofaciens subsp. kefirgranum	strain=DSM 10550	GCA_001434195.1	190906	267818	type	True	77.7734	106	662	95	below_threshold
Lactobacillus helveticus	strain=JCM 1120	GCA_015698225.1	1587	1587	type	True	77.7594	100	662	95	below_threshold
Lactobacillus acidophilus	strain=CIP 76.13	GCA_000469705.1	1579	1579	type	True	77.6167	118	662	95	below_threshold
Lactobacillus acidophilus	strain=ATCC 4356	GCA_000786395.1	1579	1579	type	True	77.5937	119	662	95	below_threshold
Lactobacillus acidophilus	strain=DSM 20079	GCA_001433895.1	1579	1579	type	True	77.5724	119	662	95	below_threshold
Lactobacillus kalixensis	strain=DSM 16043	GCA_001434335.1	227944	227944	type	True	77.5047	101	662	95	below_threshold
Lactobacillus helveticus	strain=DSM 20075	GCA_000160855.1	1587	1587	type	True	77.482	109	662	95	below_threshold
Lactobacillus helveticus	strain=CGMCC 1.1877	GCA_001434945.1	1587	1587	type	True	77.4355	98	662	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:28:32,715] [INFO] DFAST Taxonomy check result was written to GCF_019972835.1_ASM1997283v1_genomic.fna/tc_result.tsv
[2024-01-24 14:28:32,715] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:28:32,715] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:28:32,716] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49f7ac91-b3ce-4119-a13c-2ced5a19281b/dqc_reference/checkm_data
[2024-01-24 14:28:32,717] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:28:32,742] [INFO] Task started: CheckM
[2024-01-24 14:28:32,742] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019972835.1_ASM1997283v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019972835.1_ASM1997283v1_genomic.fna/checkm_input GCF_019972835.1_ASM1997283v1_genomic.fna/checkm_result
[2024-01-24 14:28:51,995] [INFO] Task succeeded: CheckM
[2024-01-24 14:28:51,999] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:28:52,016] [INFO] ===== Completeness check finished =====
[2024-01-24 14:28:52,016] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:28:52,016] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019972835.1_ASM1997283v1_genomic.fna/markers.fasta)
[2024-01-24 14:28:52,017] [INFO] Task started: Blastn
[2024-01-24 14:28:52,017] [INFO] Running command: blastn -query GCF_019972835.1_ASM1997283v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg49f7ac91-b3ce-4119-a13c-2ced5a19281b/dqc_reference/reference_markers_gtdb.fasta -out GCF_019972835.1_ASM1997283v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:28:52,800] [INFO] Task succeeded: Blastn
[2024-01-24 14:28:52,804] [INFO] Selected 5 target genomes.
[2024-01-24 14:28:52,804] [INFO] Target genome list was writen to GCF_019972835.1_ASM1997283v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:28:52,812] [INFO] Task started: fastANI
[2024-01-24 14:28:52,812] [INFO] Running command: fastANI --query /var/lib/cwl/stgb1377bd8-a492-49a0-b4a5-b11f3772df3d/GCF_019972835.1_ASM1997283v1_genomic.fna.gz --refList GCF_019972835.1_ASM1997283v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019972835.1_ASM1997283v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:28:55,596] [INFO] Task succeeded: fastANI
[2024-01-24 14:28:55,602] [INFO] Found 5 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 14:28:55,602] [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_000970755.1	s__Lactobacillus kimbladii_A	94.4583	607	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014323605.1	s__Lactobacillus kimbladii_B	93.555	522	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000967195.1	s__Lactobacillus kullabergensis	93.5364	578	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.65	96.49	0.90	0.88	4	-
GCF_016100975.1	s__Lactobacillus sp016100975	92.9116	570	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	100.00	100.00	1.00	1.00	3	-
GCF_000760615.1	s__Lactobacillus sp000760615	92.2199	551	662	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	96.94	96.94	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:28:55,603] [INFO] GTDB search result was written to GCF_019972835.1_ASM1997283v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:28:55,604] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:28:55,607] [INFO] DFAST_QC result json was written to GCF_019972835.1_ASM1997283v1_genomic.fna/dqc_result.json
[2024-01-24 14:28:55,608] [INFO] DFAST_QC completed!
[2024-01-24 14:28:55,608] [INFO] Total running time: 0h0m40s