[2024-01-25 19:54:20,738] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:54:20,740] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:54:20,740] [INFO] DQC Reference Directory: /var/lib/cwl/stg77249a31-22ff-42a4-abf2-1f376194cf14/dqc_reference
[2024-01-25 19:54:21,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:54:21,863] [INFO] Task started: Prodigal
[2024-01-25 19:54:21,864] [INFO] Running command: gunzip -c /var/lib/cwl/stgb182d61b-c909-47f8-b5ce-0f8bf11a2209/GCF_001433745.1_ASM143374v1_genomic.fna.gz | prodigal -d GCF_001433745.1_ASM143374v1_genomic.fna/cds.fna -a GCF_001433745.1_ASM143374v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:54:29,194] [INFO] Task succeeded: Prodigal
[2024-01-25 19:54:29,195] [INFO] Task started: HMMsearch
[2024-01-25 19:54:29,195] [INFO] Running command: hmmsearch --tblout GCF_001433745.1_ASM143374v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg77249a31-22ff-42a4-abf2-1f376194cf14/dqc_reference/reference_markers.hmm GCF_001433745.1_ASM143374v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:54:29,413] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:54:29,414] [INFO] Found 6/6 markers.
[2024-01-25 19:54:29,437] [INFO] Query marker FASTA was written to GCF_001433745.1_ASM143374v1_genomic.fna/markers.fasta
[2024-01-25 19:54:29,437] [INFO] Task started: Blastn
[2024-01-25 19:54:29,437] [INFO] Running command: blastn -query GCF_001433745.1_ASM143374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77249a31-22ff-42a4-abf2-1f376194cf14/dqc_reference/reference_markers.fasta -out GCF_001433745.1_ASM143374v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:29,979] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:29,981] [INFO] Selected 17 target genomes.
[2024-01-25 19:54:29,982] [INFO] Target genome list was writen to GCF_001433745.1_ASM143374v1_genomic.fna/target_genomes.txt
[2024-01-25 19:54:29,987] [INFO] Task started: fastANI
[2024-01-25 19:54:29,987] [INFO] Running command: fastANI --query /var/lib/cwl/stgb182d61b-c909-47f8-b5ce-0f8bf11a2209/GCF_001433745.1_ASM143374v1_genomic.fna.gz --refList GCF_001433745.1_ASM143374v1_genomic.fna/target_genomes.txt --output GCF_001433745.1_ASM143374v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:54:39,372] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:39,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg77249a31-22ff-42a4-abf2-1f376194cf14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:54:39,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg77249a31-22ff-42a4-abf2-1f376194cf14/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:54:39,379] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:54:39,379] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:54:39,379] [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
Lacticaseibacillus zeae	strain=DSM 20178	GCA_001433745.1	57037	57037	type	True	100.0	1011	1012	95	conclusive
Lacticaseibacillus zeae	strain=KCTC 3804	GCA_000260435.1	57037	57037	type	True	99.9571	966	1012	95	conclusive
Lacticaseibacillus casei	strain=ATCC 393	GCA_000829055.1	1582	1582	suspected-type	True	94.5241	827	1012	95	below_threshold
Lacticaseibacillus chiayiensis	strain=NCYUAS	GCA_004123795.1	2100821	2100821	type	True	88.5135	737	1012	95	below_threshold
Lacticaseibacillus rhamnosus	strain=NRRL B-442	GCA_002849515.1	47715	47715	type	True	81.0804	538	1012	95	below_threshold
Lacticaseibacillus rhamnosus	strain=NBRC 3425	GCA_007990855.1	47715	47715	type	True	80.9338	499	1012	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:54:39,381] [INFO] DFAST Taxonomy check result was written to GCF_001433745.1_ASM143374v1_genomic.fna/tc_result.tsv
[2024-01-25 19:54:39,381] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:54:39,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:54:39,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg77249a31-22ff-42a4-abf2-1f376194cf14/dqc_reference/checkm_data
[2024-01-25 19:54:39,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:54:39,415] [INFO] Task started: CheckM
[2024-01-25 19:54:39,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001433745.1_ASM143374v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001433745.1_ASM143374v1_genomic.fna/checkm_input GCF_001433745.1_ASM143374v1_genomic.fna/checkm_result
[2024-01-25 19:55:06,475] [INFO] Task succeeded: CheckM
[2024-01-25 19:55:06,476] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:55:06,523] [INFO] ===== Completeness check finished =====
[2024-01-25 19:55:06,524] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:55:06,524] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001433745.1_ASM143374v1_genomic.fna/markers.fasta)
[2024-01-25 19:55:06,524] [INFO] Task started: Blastn
[2024-01-25 19:55:06,524] [INFO] Running command: blastn -query GCF_001433745.1_ASM143374v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg77249a31-22ff-42a4-abf2-1f376194cf14/dqc_reference/reference_markers_gtdb.fasta -out GCF_001433745.1_ASM143374v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:55:07,334] [INFO] Task succeeded: Blastn
[2024-01-25 19:55:07,337] [INFO] Selected 11 target genomes.
[2024-01-25 19:55:07,337] [INFO] Target genome list was writen to GCF_001433745.1_ASM143374v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:55:07,352] [INFO] Task started: fastANI
[2024-01-25 19:55:07,353] [INFO] Running command: fastANI --query /var/lib/cwl/stgb182d61b-c909-47f8-b5ce-0f8bf11a2209/GCF_001433745.1_ASM143374v1_genomic.fna.gz --refList GCF_001433745.1_ASM143374v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001433745.1_ASM143374v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:55:15,576] [INFO] Task succeeded: fastANI
[2024-01-25 19:55:15,581] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:55:15,581] [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_000260435.1	s__Lacticaseibacillus zeae	99.9571	966	1012	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.07	96.92	0.91	0.87	11	conclusive
GCF_000829055.1	s__Lacticaseibacillus casei	94.5241	827	1012	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.76	95.69	0.93	0.80	19	-
GCF_004123795.1	s__Lacticaseibacillus chiayiensis	88.5005	738	1012	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.97	98.62	0.94	0.94	3	-
GCF_900636965.1	s__Lacticaseibacillus rhamnosus	81.1362	548	1012	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.40	96.73	0.93	0.86	237	-
GCF_000829035.1	s__Lacticaseibacillus paracasei	80.3878	453	1012	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lacticaseibacillus	95.0	98.30	97.86	0.88	0.73	252	-
--------------------------------------------------------------------------------
[2024-01-25 19:55:15,583] [INFO] GTDB search result was written to GCF_001433745.1_ASM143374v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:55:15,583] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:55:15,585] [INFO] DFAST_QC result json was written to GCF_001433745.1_ASM143374v1_genomic.fna/dqc_result.json
[2024-01-25 19:55:15,585] [INFO] DFAST_QC completed!
[2024-01-25 19:55:15,585] [INFO] Total running time: 0h0m55s