[2024-01-24 14:31:14,352] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,353] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,354] [INFO] DQC Reference Directory: /var/lib/cwl/stg5eefd82a-3d6c-4047-81b1-3d49906f58dd/dqc_reference
[2024-01-24 14:31:15,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:15,710] [INFO] Task started: Prodigal
[2024-01-24 14:31:15,710] [INFO] Running command: gunzip -c /var/lib/cwl/stgd49a0cc3-2281-4413-a269-789a834eaa7c/GCF_004354745.1_ASM435474v1_genomic.fna.gz | prodigal -d GCF_004354745.1_ASM435474v1_genomic.fna/cds.fna -a GCF_004354745.1_ASM435474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:22,330] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:22,330] [INFO] Task started: HMMsearch
[2024-01-24 14:31:22,330] [INFO] Running command: hmmsearch --tblout GCF_004354745.1_ASM435474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5eefd82a-3d6c-4047-81b1-3d49906f58dd/dqc_reference/reference_markers.hmm GCF_004354745.1_ASM435474v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:22,628] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:22,629] [INFO] Found 6/6 markers.
[2024-01-24 14:31:22,678] [INFO] Query marker FASTA was written to GCF_004354745.1_ASM435474v1_genomic.fna/markers.fasta
[2024-01-24 14:31:22,678] [INFO] Task started: Blastn
[2024-01-24 14:31:22,679] [INFO] Running command: blastn -query GCF_004354745.1_ASM435474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5eefd82a-3d6c-4047-81b1-3d49906f58dd/dqc_reference/reference_markers.fasta -out GCF_004354745.1_ASM435474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:23,344] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:23,347] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:23,348] [INFO] Target genome list was writen to GCF_004354745.1_ASM435474v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:23,352] [INFO] Task started: fastANI
[2024-01-24 14:31:23,352] [INFO] Running command: fastANI --query /var/lib/cwl/stgd49a0cc3-2281-4413-a269-789a834eaa7c/GCF_004354745.1_ASM435474v1_genomic.fna.gz --refList GCF_004354745.1_ASM435474v1_genomic.fna/target_genomes.txt --output GCF_004354745.1_ASM435474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:29,582] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:29,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5eefd82a-3d6c-4047-81b1-3d49906f58dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:29,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5eefd82a-3d6c-4047-81b1-3d49906f58dd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:29,602] [INFO] Found 10 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 14:31:29,603] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:29,603] [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 buchneri	strain=ATCC 4005	GCA_004354745.1	1581	1581	type	True	100.0	809	812	95	conclusive
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_018314255.1	1581	1581	type	True	99.9612	805	812	95	conclusive
Lentilactobacillus buchneri	strain=DSM 20057	GCA_001434735.1	1581	1581	type	True	99.9526	758	812	95	conclusive
Lentilactobacillus buchneri	strain=ATCC 4005	GCA_009495475.1	1581	1581	type	True	99.9175	796	812	95	conclusive
Lentilactobacillus buchneri subsp. silagei	strain=SG162	GCA_013167835.1	2737512	1581	type	True	97.1486	753	812	95	conclusive
Lentilactobacillus otakiensis	strain=JCM 15040	GCA_001311395.1	481720	481720	type	True	83.3529	540	812	95	below_threshold
Lentilactobacillus rapi subsp. rapi	strain=JCM 15042	GCA_001311445.1	2944812	481723	type	True	78.8469	250	812	95	below_threshold
Secundilactobacillus silagei	strain=DSM 27022	GCA_004354595.1	1293415	1293415	type	True	78.1213	68	812	95	below_threshold
Secundilactobacillus silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	77.6237	66	812	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	77.6024	66	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:29,607] [INFO] DFAST Taxonomy check result was written to GCF_004354745.1_ASM435474v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:29,609] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:29,610] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:29,610] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5eefd82a-3d6c-4047-81b1-3d49906f58dd/dqc_reference/checkm_data
[2024-01-24 14:31:29,611] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:29,655] [INFO] Task started: CheckM
[2024-01-24 14:31:29,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004354745.1_ASM435474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004354745.1_ASM435474v1_genomic.fna/checkm_input GCF_004354745.1_ASM435474v1_genomic.fna/checkm_result
[2024-01-24 14:31:57,043] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:57,045] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:57,066] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:57,066] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:57,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004354745.1_ASM435474v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:57,067] [INFO] Task started: Blastn
[2024-01-24 14:31:57,067] [INFO] Running command: blastn -query GCF_004354745.1_ASM435474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5eefd82a-3d6c-4047-81b1-3d49906f58dd/dqc_reference/reference_markers_gtdb.fasta -out GCF_004354745.1_ASM435474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:57,903] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:57,908] [INFO] Selected 10 target genomes.
[2024-01-24 14:31:57,909] [INFO] Target genome list was writen to GCF_004354745.1_ASM435474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:57,918] [INFO] Task started: fastANI
[2024-01-24 14:31:57,918] [INFO] Running command: fastANI --query /var/lib/cwl/stgd49a0cc3-2281-4413-a269-789a834eaa7c/GCF_004354745.1_ASM435474v1_genomic.fna.gz --refList GCF_004354745.1_ASM435474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004354745.1_ASM435474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:04,545] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:04,557] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:04,558] [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_018314255.1	s__Lentilactobacillus buchneri	99.9612	805	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.61	97.12	0.94	0.90	27	conclusive
GCF_002157585.1	s__Lentilactobacillus parakefiri	85.6525	605	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.70	99.39	0.94	0.92	4	-
GCF_001434145.1	s__Lentilactobacillus otakiensis	83.4117	548	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.95	99.91	1.00	1.00	3	-
GCF_007989105.1	s__Lentilactobacillus kefiri	82.2239	473	812	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	82.1697	531	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	96.44	96.44	0.90	0.90	2	-
GCF_001435315.1	s__Lentilactobacillus parabuchneri	81.7619	458	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	98.90	97.37	0.94	0.87	27	-
GCF_001436255.1	s__Lentilactobacillus rapi	78.8556	259	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lentilactobacillus	95.0	99.94	99.89	1.00	1.00	3	-
GCF_002217925.1	s__Secundilactobacillus mixtipabuli	77.6533	69	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:32:04,560] [INFO] GTDB search result was written to GCF_004354745.1_ASM435474v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:04,561] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:04,564] [INFO] DFAST_QC result json was written to GCF_004354745.1_ASM435474v1_genomic.fna/dqc_result.json
[2024-01-24 14:32:04,564] [INFO] DFAST_QC completed!
[2024-01-24 14:32:04,564] [INFO] Total running time: 0h0m50s