[2024-01-24 14:19:18,317] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:19:18,321] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:19:18,322] [INFO] DQC Reference Directory: /var/lib/cwl/stg29d9501c-c1ed-435f-b876-aab119fd0985/dqc_reference
[2024-01-24 14:19:19,639] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:19:19,640] [INFO] Task started: Prodigal
[2024-01-24 14:19:19,640] [INFO] Running command: gunzip -c /var/lib/cwl/stgef41ce92-e250-4941-bc70-45272d4d79fb/GCF_004354795.1_ASM435479v1_genomic.fna.gz | prodigal -d GCF_004354795.1_ASM435479v1_genomic.fna/cds.fna -a GCF_004354795.1_ASM435479v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:19:25,944] [INFO] Task succeeded: Prodigal
[2024-01-24 14:19:25,944] [INFO] Task started: HMMsearch
[2024-01-24 14:19:25,944] [INFO] Running command: hmmsearch --tblout GCF_004354795.1_ASM435479v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg29d9501c-c1ed-435f-b876-aab119fd0985/dqc_reference/reference_markers.hmm GCF_004354795.1_ASM435479v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:19:26,229] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:19:26,235] [INFO] Found 6/6 markers.
[2024-01-24 14:19:26,271] [INFO] Query marker FASTA was written to GCF_004354795.1_ASM435479v1_genomic.fna/markers.fasta
[2024-01-24 14:19:26,271] [INFO] Task started: Blastn
[2024-01-24 14:19:26,272] [INFO] Running command: blastn -query GCF_004354795.1_ASM435479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d9501c-c1ed-435f-b876-aab119fd0985/dqc_reference/reference_markers.fasta -out GCF_004354795.1_ASM435479v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:19:26,935] [INFO] Task succeeded: Blastn
[2024-01-24 14:19:26,942] [INFO] Selected 14 target genomes.
[2024-01-24 14:19:26,942] [INFO] Target genome list was writen to GCF_004354795.1_ASM435479v1_genomic.fna/target_genomes.txt
[2024-01-24 14:19:26,954] [INFO] Task started: fastANI
[2024-01-24 14:19:26,954] [INFO] Running command: fastANI --query /var/lib/cwl/stgef41ce92-e250-4941-bc70-45272d4d79fb/GCF_004354795.1_ASM435479v1_genomic.fna.gz --refList GCF_004354795.1_ASM435479v1_genomic.fna/target_genomes.txt --output GCF_004354795.1_ASM435479v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:19:33,790] [INFO] Task succeeded: fastANI
[2024-01-24 14:19:33,790] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg29d9501c-c1ed-435f-b876-aab119fd0985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:19:33,790] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg29d9501c-c1ed-435f-b876-aab119fd0985/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:19:33,800] [INFO] Found 11 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:19:33,800] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:19:33,800] [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
Lentilactobacillus hilgardii	strain=ATCC 8290	GCA_004354795.1	1588	1588	type	True	100.0	873	879	95	conclusive
Lentilactobacillus hilgardii	strain=DSM 20176	GCA_001434655.1	1588	1588	type	True	99.9134	801	879	95	conclusive
Lentilactobacillus hilgardii	strain=ATCC 8290	GCA_000159315.1	1588	1588	type	True	99.8076	858	879	95	conclusive
Lentilactobacillus farraginis	strain=DSM 18382	GCA_001435875.1	390841	390841	type	True	80.9013	472	879	95	below_threshold
Lentilactobacillus farraginis	strain=JCM 14108	GCA_000583655.1	390841	390841	type	True	80.798	476	879	95	below_threshold
Lentilactobacillus otakiensis	strain=DSM 19908	GCA_001434145.1	481720	481720	type	True	79.3192	207	879	95	below_threshold
Lentilactobacillus parakefiri	strain=DSM 10551	GCA_004354625.1	152332	152332	type	True	79.2825	179	879	95	below_threshold
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_000415925.1	481720	481720	type	True	79.2358	204	879	95	below_threshold
Lentilactobacillus laojiaonis	strain=IM3328	GCA_020616595.1	2883998	2883998	type	True	79.2307	55	879	95	below_threshold
Lentilactobacillus parakefiri	strain=JCM 8573	GCA_002157585.1	152332	152332	type	True	79.205	180	879	95	below_threshold
Lentilactobacillus kisonensis	strain=JCM 15041	GCA_001311425.1	481722	481722	type	True	78.8861	171	879	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:19:33,802] [INFO] DFAST Taxonomy check result was written to GCF_004354795.1_ASM435479v1_genomic.fna/tc_result.tsv
[2024-01-24 14:19:33,802] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:19:33,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:19:33,803] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg29d9501c-c1ed-435f-b876-aab119fd0985/dqc_reference/checkm_data
[2024-01-24 14:19:33,804] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:19:33,834] [INFO] Task started: CheckM
[2024-01-24 14:19:33,834] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354795.1_ASM435479v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354795.1_ASM435479v1_genomic.fna/checkm_input GCF_004354795.1_ASM435479v1_genomic.fna/checkm_result
[2024-01-24 14:20:00,909] [INFO] Task succeeded: CheckM
[2024-01-24 14:20:00,910] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:20:00,932] [INFO] ===== Completeness check finished =====
[2024-01-24 14:20:00,932] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:20:00,933] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354795.1_ASM435479v1_genomic.fna/markers.fasta)
[2024-01-24 14:20:00,933] [INFO] Task started: Blastn
[2024-01-24 14:20:00,933] [INFO] Running command: blastn -query GCF_004354795.1_ASM435479v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg29d9501c-c1ed-435f-b876-aab119fd0985/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354795.1_ASM435479v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:20:01,743] [INFO] Task succeeded: Blastn
[2024-01-24 14:20:01,747] [INFO] Selected 22 target genomes.
[2024-01-24 14:20:01,747] [INFO] Target genome list was writen to GCF_004354795.1_ASM435479v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:20:01,763] [INFO] Task started: fastANI
[2024-01-24 14:20:01,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgef41ce92-e250-4941-bc70-45272d4d79fb/GCF_004354795.1_ASM435479v1_genomic.fna.gz --refList GCF_004354795.1_ASM435479v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354795.1_ASM435479v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:20:11,220] [INFO] Task succeeded: fastANI
[2024-01-24 14:20:11,232] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:20:11,232] [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_000159315.1	s__Lentilactobacillus hilgardii	99.8076	858	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.37	96.88	0.92	0.87	10	conclusive
GCF_000583655.1	s__Lentilactobacillus farraginis	80.8009	477	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
GCF_018314255.1	s__Lentilactobacillus buchneri	79.9716	193	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	-
GCF_900411375.1	s__Lentilactobacillus raoultii	79.7456	391	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435895.1	s__Lentilactobacillus parafarraginis	79.6713	300	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.53	97.19	0.92	0.88	5	-
GCF_019061365.1	s__Lentilactobacillus sp019061365	79.5874	194	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.43	99.43	0.89	0.89	2	-
GCF_007989105.1	s__Lentilactobacillus kefiri	79.4615	216	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.76	99.64	0.95	0.93	9	-
GCF_001435575.1	s__Lentilactobacillus sunkii	79.4343	196	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	79.2728	209	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCF_002157585.1	s__Lentilactobacillus parakefiri	79.1389	179	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
GCF_001435315.1	s__Lentilactobacillus parabuchneri	78.9521	210	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.90	97.37	0.94	0.87	27	-
GCF_001434135.1	s__Lentilactobacillus kisonensis	78.9495	166	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.52	0.95	0.93	3	-
GCF_001436255.1	s__Lentilactobacillus rapi	78.3188	180	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.94	99.89	1.00	1.00	3	-
GCF_016860605.1	s__Lentilactobacillus sp016860605	78.1879	158	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002993975.1	s__Apilactobacillus micheneri	77.3819	50	879	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Apilactobacillus	95.0	98.16	96.49	0.93	0.89	21	-
--------------------------------------------------------------------------------
[2024-01-24 14:20:11,234] [INFO] GTDB search result was written to GCF_004354795.1_ASM435479v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:20:11,235] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:20:11,238] [INFO] DFAST_QC result json was written to GCF_004354795.1_ASM435479v1_genomic.fna/dqc_result.json
[2024-01-24 14:20:11,238] [INFO] DFAST_QC completed!
[2024-01-24 14:20:11,238] [INFO] Total running time: 0h0m53s