[2024-01-25 19:59:05,512] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:59:05,520] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:59:05,521] [INFO] DQC Reference Directory: /var/lib/cwl/stgc7d4ad25-fea3-4e9f-b0f0-ee9653312ee6/dqc_reference
[2024-01-25 19:59:06,715] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:59:06,716] [INFO] Task started: Prodigal
[2024-01-25 19:59:06,716] [INFO] Running command: gunzip -c /var/lib/cwl/stgc6128c43-02d4-4124-8917-7db41ed14b3b/GCF_024345185.1_ASM2434518v1_genomic.fna.gz | prodigal -d GCF_024345185.1_ASM2434518v1_genomic.fna/cds.fna -a GCF_024345185.1_ASM2434518v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:59:11,786] [INFO] Task succeeded: Prodigal
[2024-01-25 19:59:11,786] [INFO] Task started: HMMsearch
[2024-01-25 19:59:11,786] [INFO] Running command: hmmsearch --tblout GCF_024345185.1_ASM2434518v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc7d4ad25-fea3-4e9f-b0f0-ee9653312ee6/dqc_reference/reference_markers.hmm GCF_024345185.1_ASM2434518v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:59:12,000] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:59:12,001] [INFO] Found 6/6 markers.
[2024-01-25 19:59:12,022] [INFO] Query marker FASTA was written to GCF_024345185.1_ASM2434518v1_genomic.fna/markers.fasta
[2024-01-25 19:59:12,022] [INFO] Task started: Blastn
[2024-01-25 19:59:12,022] [INFO] Running command: blastn -query GCF_024345185.1_ASM2434518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7d4ad25-fea3-4e9f-b0f0-ee9653312ee6/dqc_reference/reference_markers.fasta -out GCF_024345185.1_ASM2434518v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:12,579] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:12,582] [INFO] Selected 15 target genomes.
[2024-01-25 19:59:12,583] [INFO] Target genome list was writen to GCF_024345185.1_ASM2434518v1_genomic.fna/target_genomes.txt
[2024-01-25 19:59:12,591] [INFO] Task started: fastANI
[2024-01-25 19:59:12,591] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6128c43-02d4-4124-8917-7db41ed14b3b/GCF_024345185.1_ASM2434518v1_genomic.fna.gz --refList GCF_024345185.1_ASM2434518v1_genomic.fna/target_genomes.txt --output GCF_024345185.1_ASM2434518v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:59:20,264] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:20,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc7d4ad25-fea3-4e9f-b0f0-ee9653312ee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:59:20,265] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc7d4ad25-fea3-4e9f-b0f0-ee9653312ee6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:59:20,275] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:59:20,275] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:59:20,275] [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 paucivorans	strain=DSM 22467	GCA_001437125.1	616990	616990	type	True	93.1342	656	760	95	below_threshold
Levilactobacillus lindianensis	strain=220-4	GCA_003946095.1	2486018	2486018	type	True	89.8557	653	760	95	below_threshold
Levilactobacillus huananensis	strain=151-2B	GCA_003946145.1	2486019	2486019	type	True	88.2226	629	760	95	below_threshold
Levilactobacillus parabrevis	strain=LMG 11984	GCA_001437515.1	357278	357278	type	True	81.2656	389	760	95	below_threshold
Levilactobacillus parabrevis	strain=ATCC 53295	GCA_001434055.1	357278	357278	type	True	81.2181	376	760	95	below_threshold
Levilactobacillus fuyuanensis	strain=244-4	GCA_003946395.1	2486022	2486022	type	True	81.0363	402	760	95	below_threshold
Levilactobacillus hammesii	strain=DSM 16381	GCA_001434395.1	267633	267633	type	True	81.0224	365	760	95	below_threshold
Levilactobacillus andaensis	strain=866-3	GCA_016861695.1	2799570	2799570	type	True	80.818	362	760	95	below_threshold
Levilactobacillus lanxiensis	strain=13B17	GCA_016861655.1	2799568	2799568	type	True	80.5872	366	760	95	below_threshold
Levilactobacillus tangyuanensis	strain=137-3	GCA_003946545.1	2486021	2486021	type	True	80.1096	308	760	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	79.0133	68	760	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:59:20,277] [INFO] DFAST Taxonomy check result was written to GCF_024345185.1_ASM2434518v1_genomic.fna/tc_result.tsv
[2024-01-25 19:59:20,281] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:59:20,281] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:59:20,282] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc7d4ad25-fea3-4e9f-b0f0-ee9653312ee6/dqc_reference/checkm_data
[2024-01-25 19:59:20,283] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:59:20,309] [INFO] Task started: CheckM
[2024-01-25 19:59:20,310] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024345185.1_ASM2434518v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024345185.1_ASM2434518v1_genomic.fna/checkm_input GCF_024345185.1_ASM2434518v1_genomic.fna/checkm_result
[2024-01-25 19:59:41,153] [INFO] Task succeeded: CheckM
[2024-01-25 19:59:41,154] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:59:41,168] [INFO] ===== Completeness check finished =====
[2024-01-25 19:59:41,168] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:59:41,169] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024345185.1_ASM2434518v1_genomic.fna/markers.fasta)
[2024-01-25 19:59:41,169] [INFO] Task started: Blastn
[2024-01-25 19:59:41,169] [INFO] Running command: blastn -query GCF_024345185.1_ASM2434518v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc7d4ad25-fea3-4e9f-b0f0-ee9653312ee6/dqc_reference/reference_markers_gtdb.fasta -out GCF_024345185.1_ASM2434518v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:59:41,941] [INFO] Task succeeded: Blastn
[2024-01-25 19:59:41,944] [INFO] Selected 12 target genomes.
[2024-01-25 19:59:41,944] [INFO] Target genome list was writen to GCF_024345185.1_ASM2434518v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:59:41,960] [INFO] Task started: fastANI
[2024-01-25 19:59:41,960] [INFO] Running command: fastANI --query /var/lib/cwl/stgc6128c43-02d4-4124-8917-7db41ed14b3b/GCF_024345185.1_ASM2434518v1_genomic.fna.gz --refList GCF_024345185.1_ASM2434518v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024345185.1_ASM2434518v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:59:49,463] [INFO] Task succeeded: fastANI
[2024-01-25 19:59:49,471] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:59:49,472] [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_001437125.1	s__Levilactobacillus paucivorans	93.1342	656	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946095.1	s__Levilactobacillus lindianensis	89.8557	653	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946145.1	s__Levilactobacillus huananensis	88.2407	628	760	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	81.206	377	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.99	99.98	0.99	0.98	3	-
GCF_001434395.1	s__Levilactobacillus hammesii	81.0224	365	760	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	81.0196	404	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861695.1	s__Levilactobacillus sp016861695	80.8212	363	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012641095.1	s__Levilactobacillus sp012641095	80.755	348	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003666485.1	s__Levilactobacillus brevis_A	80.7109	346	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861585.1	s__Levilactobacillus sp016861585	80.6346	375	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
GCF_012641185.1	s__Levilactobacillus sp012641185	80.5104	321	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	95.99	95.94	0.88	0.87	3	-
GCF_003946545.1	s__Levilactobacillus tangyuanensis	80.1407	309	760	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:59:49,473] [INFO] GTDB search result was written to GCF_024345185.1_ASM2434518v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:59:49,474] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:59:49,477] [INFO] DFAST_QC result json was written to GCF_024345185.1_ASM2434518v1_genomic.fna/dqc_result.json
[2024-01-25 19:59:49,477] [INFO] DFAST_QC completed!
[2024-01-25 19:59:49,477] [INFO] Total running time: 0h0m44s