[2024-01-24 14:06:06,872] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:06,873] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:06,874] [INFO] DQC Reference Directory: /var/lib/cwl/stgdbbd6b9f-8870-4204-b827-546b13b9933f/dqc_reference
[2024-01-24 14:06:08,367] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:08,369] [INFO] Task started: Prodigal
[2024-01-24 14:06:08,369] [INFO] Running command: gunzip -c /var/lib/cwl/stg421cedc9-0819-4707-a1c1-375e604dfcf3/GCF_012641185.1_ASM1264118v1_genomic.fna.gz | prodigal -d GCF_012641185.1_ASM1264118v1_genomic.fna/cds.fna -a GCF_012641185.1_ASM1264118v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:15,194] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:15,194] [INFO] Task started: HMMsearch
[2024-01-24 14:06:15,194] [INFO] Running command: hmmsearch --tblout GCF_012641185.1_ASM1264118v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdbbd6b9f-8870-4204-b827-546b13b9933f/dqc_reference/reference_markers.hmm GCF_012641185.1_ASM1264118v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:15,498] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:15,499] [INFO] Found 6/6 markers.
[2024-01-24 14:06:15,524] [INFO] Query marker FASTA was written to GCF_012641185.1_ASM1264118v1_genomic.fna/markers.fasta
[2024-01-24 14:06:15,525] [INFO] Task started: Blastn
[2024-01-24 14:06:15,525] [INFO] Running command: blastn -query GCF_012641185.1_ASM1264118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbbd6b9f-8870-4204-b827-546b13b9933f/dqc_reference/reference_markers.fasta -out GCF_012641185.1_ASM1264118v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:16,155] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:16,160] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:16,160] [INFO] Target genome list was writen to GCF_012641185.1_ASM1264118v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:16,165] [INFO] Task started: fastANI
[2024-01-24 14:06:16,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg421cedc9-0819-4707-a1c1-375e604dfcf3/GCF_012641185.1_ASM1264118v1_genomic.fna.gz --refList GCF_012641185.1_ASM1264118v1_genomic.fna/target_genomes.txt --output GCF_012641185.1_ASM1264118v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:26,951] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:26,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdbbd6b9f-8870-4204-b827-546b13b9933f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:26,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdbbd6b9f-8870-4204-b827-546b13b9933f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:26,960] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:26,960] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:26,961] [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
Levilactobacillus tujiorum	strain=HBUAS51241	GCA_012641185.1	2912243	2912243	type	True	100.0	843	843	95	conclusive
Levilactobacillus hammesii	strain=DSM 16381	GCA_001434395.1	267633	267633	type	True	83.8876	582	843	95	below_threshold
Levilactobacillus parabrevis	strain=ATCC 53295	GCA_001434055.1	357278	357278	type	True	82.9756	527	843	95	below_threshold
Levilactobacillus parabrevis	strain=LMG 11984	GCA_001437515.1	357278	357278	type	True	82.9314	530	843	95	below_threshold
Levilactobacillus parabrevis	strain=RODS-DW	GCA_000383435.1	357278	357278	type	True	82.8708	530	843	95	below_threshold
Levilactobacillus fuyuanensis	strain=244-4	GCA_003946395.1	2486022	2486022	type	True	82.7623	535	843	95	below_threshold
Levilactobacillus koreensis	strain=JCM 16448	GCA_001435525.1	637971	637971	type	True	80.807	359	843	95	below_threshold
Levilactobacillus tongjiangensis	strain=218-10	GCA_003946345.1	2486023	2486023	type	True	80.7779	340	843	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:26,965] [INFO] DFAST Taxonomy check result was written to GCF_012641185.1_ASM1264118v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:26,967] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:26,968] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:26,968] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdbbd6b9f-8870-4204-b827-546b13b9933f/dqc_reference/checkm_data
[2024-01-24 14:06:26,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:27,000] [INFO] Task started: CheckM
[2024-01-24 14:06:27,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012641185.1_ASM1264118v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012641185.1_ASM1264118v1_genomic.fna/checkm_input GCF_012641185.1_ASM1264118v1_genomic.fna/checkm_result
[2024-01-24 14:06:54,047] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:54,048] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:54,073] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:54,073] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:54,073] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012641185.1_ASM1264118v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:54,074] [INFO] Task started: Blastn
[2024-01-24 14:06:54,074] [INFO] Running command: blastn -query GCF_012641185.1_ASM1264118v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdbbd6b9f-8870-4204-b827-546b13b9933f/dqc_reference/reference_markers_gtdb.fasta -out GCF_012641185.1_ASM1264118v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:54,907] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:54,911] [INFO] Selected 6 target genomes.
[2024-01-24 14:06:54,911] [INFO] Target genome list was writen to GCF_012641185.1_ASM1264118v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:54,915] [INFO] Task started: fastANI
[2024-01-24 14:06:54,915] [INFO] Running command: fastANI --query /var/lib/cwl/stg421cedc9-0819-4707-a1c1-375e604dfcf3/GCF_012641185.1_ASM1264118v1_genomic.fna.gz --refList GCF_012641185.1_ASM1264118v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012641185.1_ASM1264118v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:00,160] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:00,167] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:00,167] [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_012641185.1	s__Levilactobacillus sp012641185	100.0	843	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.99	95.94	0.88	0.87	3	conclusive
GCF_001434395.1	s__Levilactobacillus hammesii	83.8483	584	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434055.1	s__Levilactobacillus parabrevis	82.9711	527	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.99	99.98	0.99	0.98	3	-
GCF_012641095.1	s__Levilactobacillus sp012641095	82.9679	525	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946395.1	s__Levilactobacillus fuyuanensis	82.7807	534	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435525.1	s__Levilactobacillus koreensis	80.7558	363	843	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.98	99.98	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:00,169] [INFO] GTDB search result was written to GCF_012641185.1_ASM1264118v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:00,169] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:00,172] [INFO] DFAST_QC result json was written to GCF_012641185.1_ASM1264118v1_genomic.fna/dqc_result.json
[2024-01-24 14:07:00,172] [INFO] DFAST_QC completed!
[2024-01-24 14:07:00,172] [INFO] Total running time: 0h0m53s