[2024-01-25 19:39:50,845] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:39:50,847] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:39:50,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgf7bbd88e-df25-470c-8b63-0f48b841d3b1/dqc_reference
[2024-01-25 19:39:52,020] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:39:52,020] [INFO] Task started: Prodigal
[2024-01-25 19:39:52,021] [INFO] Running command: gunzip -c /var/lib/cwl/stg48559d9a-56c0-4d19-ab51-8308edbf95fe/GCF_000612445.1_ASM61244v1_genomic.fna.gz | prodigal -d GCF_000612445.1_ASM61244v1_genomic.fna/cds.fna -a GCF_000612445.1_ASM61244v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:39:56,692] [INFO] Task succeeded: Prodigal
[2024-01-25 19:39:56,692] [INFO] Task started: HMMsearch
[2024-01-25 19:39:56,692] [INFO] Running command: hmmsearch --tblout GCF_000612445.1_ASM61244v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf7bbd88e-df25-470c-8b63-0f48b841d3b1/dqc_reference/reference_markers.hmm GCF_000612445.1_ASM61244v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:39:56,901] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:39:56,902] [INFO] Found 6/6 markers.
[2024-01-25 19:39:56,923] [INFO] Query marker FASTA was written to GCF_000612445.1_ASM61244v1_genomic.fna/markers.fasta
[2024-01-25 19:39:56,923] [INFO] Task started: Blastn
[2024-01-25 19:39:56,923] [INFO] Running command: blastn -query GCF_000612445.1_ASM61244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7bbd88e-df25-470c-8b63-0f48b841d3b1/dqc_reference/reference_markers.fasta -out GCF_000612445.1_ASM61244v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:39:57,459] [INFO] Task succeeded: Blastn
[2024-01-25 19:39:57,462] [INFO] Selected 22 target genomes.
[2024-01-25 19:39:57,463] [INFO] Target genome list was writen to GCF_000612445.1_ASM61244v1_genomic.fna/target_genomes.txt
[2024-01-25 19:39:57,475] [INFO] Task started: fastANI
[2024-01-25 19:39:57,475] [INFO] Running command: fastANI --query /var/lib/cwl/stg48559d9a-56c0-4d19-ab51-8308edbf95fe/GCF_000612445.1_ASM61244v1_genomic.fna.gz --refList GCF_000612445.1_ASM61244v1_genomic.fna/target_genomes.txt --output GCF_000612445.1_ASM61244v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:40:06,761] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:06,761] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf7bbd88e-df25-470c-8b63-0f48b841d3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:40:06,762] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf7bbd88e-df25-470c-8b63-0f48b841d3b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:40:06,767] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:40:06,768] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:40:06,768] [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
Liquorilactobacillus sucicola	strain=JCM 15457	GCA_000612445.1	519050	519050	type	True	100.0	812	812	95	conclusive
Liquorilactobacillus sucicola	strain=DSM 21376	GCA_001436705.1	519050	519050	type	True	99.9737	812	812	95	conclusive
Liquorilactobacillus aquaticus	strain=DSM 21051	GCA_001436755.1	392566	392566	type	True	80.5468	426	812	95	below_threshold
Liquorilactobacillus uvarum	strain=DSM 19971	GCA_001434935.1	303240	303240	type	True	80.3765	428	812	95	below_threshold
Liquorilactobacillus capillatus	strain=DSM 19910	GCA_001434915.1	480931	480931	type	True	80.1378	334	812	95	below_threshold
Liquorilactobacillus nagelii	strain=DSM 13675	GCA_019444005.1	82688	82688	type	True	78.022	96	812	95	below_threshold
Liquorilactobacillus nagelii	strain=DSM 13675	GCA_001434225.1	82688	82688	type	True	77.7554	91	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:40:06,769] [INFO] DFAST Taxonomy check result was written to GCF_000612445.1_ASM61244v1_genomic.fna/tc_result.tsv
[2024-01-25 19:40:06,770] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:40:06,770] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:40:06,770] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf7bbd88e-df25-470c-8b63-0f48b841d3b1/dqc_reference/checkm_data
[2024-01-25 19:40:06,771] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:40:06,813] [INFO] Task started: CheckM
[2024-01-25 19:40:06,813] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000612445.1_ASM61244v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000612445.1_ASM61244v1_genomic.fna/checkm_input GCF_000612445.1_ASM61244v1_genomic.fna/checkm_result
[2024-01-25 19:40:26,746] [INFO] Task succeeded: CheckM
[2024-01-25 19:40:26,747] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:40:26,768] [INFO] ===== Completeness check finished =====
[2024-01-25 19:40:26,768] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:40:26,769] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000612445.1_ASM61244v1_genomic.fna/markers.fasta)
[2024-01-25 19:40:26,769] [INFO] Task started: Blastn
[2024-01-25 19:40:26,769] [INFO] Running command: blastn -query GCF_000612445.1_ASM61244v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf7bbd88e-df25-470c-8b63-0f48b841d3b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_000612445.1_ASM61244v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:40:27,496] [INFO] Task succeeded: Blastn
[2024-01-25 19:40:27,498] [INFO] Selected 25 target genomes.
[2024-01-25 19:40:27,499] [INFO] Target genome list was writen to GCF_000612445.1_ASM61244v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:40:27,537] [INFO] Task started: fastANI
[2024-01-25 19:40:27,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg48559d9a-56c0-4d19-ab51-8308edbf95fe/GCF_000612445.1_ASM61244v1_genomic.fna.gz --refList GCF_000612445.1_ASM61244v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000612445.1_ASM61244v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:40:38,743] [INFO] Task succeeded: fastANI
[2024-01-25 19:40:38,749] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:40:38,750] [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_000612445.1	s__Liquorilactobacillus sucicola	100.0	812	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_001436755.1	s__Liquorilactobacillus aquaticus	80.5511	426	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434935.1	s__Liquorilactobacillus uvarum	80.3765	428	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434915.1	s__Liquorilactobacillus capillatus	80.1524	333	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436735.1	s__Liquorilactobacillus cacaonum	77.959	90	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434225.1	s__Liquorilactobacillus nagelii	77.7656	90	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.67	98.67	0.89	0.89	2	-
GCF_001435235.1	s__Liquorilactobacillus ghanensis	77.7201	93	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905204935.1	s__Ligilactobacillus sp900765635	77.297	53	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:40:38,751] [INFO] GTDB search result was written to GCF_000612445.1_ASM61244v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:40:38,751] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:40:38,758] [INFO] DFAST_QC result json was written to GCF_000612445.1_ASM61244v1_genomic.fna/dqc_result.json
[2024-01-25 19:40:38,758] [INFO] DFAST_QC completed!
[2024-01-25 19:40:38,758] [INFO] Total running time: 0h0m48s