[2024-01-25 18:59:05,969] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:59:05,970] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:59:05,971] [INFO] DQC Reference Directory: /var/lib/cwl/stgdca46cd0-0b91-48ea-865c-44bf4bb5b748/dqc_reference
[2024-01-25 18:59:07,151] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:59:07,152] [INFO] Task started: Prodigal
[2024-01-25 18:59:07,152] [INFO] Running command: gunzip -c /var/lib/cwl/stg037e8617-f3c5-47b6-9df8-371af8397810/GCF_000498955.2_NMG01_genomic.fna.gz | prodigal -d GCF_000498955.2_NMG01_genomic.fna/cds.fna -a GCF_000498955.2_NMG01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:59:13,254] [INFO] Task succeeded: Prodigal
[2024-01-25 18:59:13,254] [INFO] Task started: HMMsearch
[2024-01-25 18:59:13,254] [INFO] Running command: hmmsearch --tblout GCF_000498955.2_NMG01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdca46cd0-0b91-48ea-865c-44bf4bb5b748/dqc_reference/reference_markers.hmm GCF_000498955.2_NMG01_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:59:13,463] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:59:13,464] [INFO] Found 6/6 markers.
[2024-01-25 18:59:13,490] [INFO] Query marker FASTA was written to GCF_000498955.2_NMG01_genomic.fna/markers.fasta
[2024-01-25 18:59:13,491] [INFO] Task started: Blastn
[2024-01-25 18:59:13,491] [INFO] Running command: blastn -query GCF_000498955.2_NMG01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca46cd0-0b91-48ea-865c-44bf4bb5b748/dqc_reference/reference_markers.fasta -out GCF_000498955.2_NMG01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:14,049] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:14,052] [INFO] Selected 18 target genomes.
[2024-01-25 18:59:14,052] [INFO] Target genome list was writen to GCF_000498955.2_NMG01_genomic.fna/target_genomes.txt
[2024-01-25 18:59:14,073] [INFO] Task started: fastANI
[2024-01-25 18:59:14,073] [INFO] Running command: fastANI --query /var/lib/cwl/stg037e8617-f3c5-47b6-9df8-371af8397810/GCF_000498955.2_NMG01_genomic.fna.gz --refList GCF_000498955.2_NMG01_genomic.fna/target_genomes.txt --output GCF_000498955.2_NMG01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:59:24,558] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:24,558] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdca46cd0-0b91-48ea-865c-44bf4bb5b748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:59:24,558] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdca46cd0-0b91-48ea-865c-44bf4bb5b748/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:59:24,567] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:59:24,567] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:59:24,567] [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
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	100.0	1002	1010	95	conclusive
Lactiplantibacillus dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	80.5202	386	1010	95	below_threshold
Lactiplantibacillus daowaiensis	strain=203-3	GCA_005405085.1	2559918	2559918	type	True	80.4918	405	1010	95	below_threshold
Lactiplantibacillus nangangensis	strain=381-7	GCA_005405065.1	2559917	2559917	type	True	80.4666	413	1010	95	below_threshold
Lactiplantibacillus daoliensis	strain=116-1A	GCA_005405005.1	2559916	2559916	type	True	80.4159	389	1010	95	below_threshold
Lactiplantibacillus songbeiensis	strain=398-2	GCA_005405125.1	2559920	2559920	type	True	80.4043	379	1010	95	below_threshold
Lactiplantibacillus pingfangensis	strain=382-1	GCA_005404945.1	2559915	2559915	type	True	80.1252	393	1010	95	below_threshold
Lactiplantibacillus xiangfangensis	strain=LMG 26013	GCA_001438845.1	942150	942150	type	True	80.1233	388	1010	95	below_threshold
Lactiplantibacillus garii	strain=FI11369	GCA_003885105.1	2306423	2306423	type	True	79.9108	353	1010	95	below_threshold
Lactiplantibacillus modestisalitolerans	strain=NBRC 107235	GCA_005405425.1	1457219	1457219	type	True	79.6219	290	1010	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	78.9716	61	1010	95	below_threshold
Secundilactobacillus silagei	strain=JCM 19001	GCA_001313225.1	1293415	1293415	type	True	78.1133	57	1010	95	below_threshold
Agrilactobacillus composti	strain=JCM 14202	GCA_000583695.1	398555	398555	type	True	76.8004	50	1010	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:59:24,568] [INFO] DFAST Taxonomy check result was written to GCF_000498955.2_NMG01_genomic.fna/tc_result.tsv
[2024-01-25 18:59:24,569] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:59:24,569] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:59:24,569] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdca46cd0-0b91-48ea-865c-44bf4bb5b748/dqc_reference/checkm_data
[2024-01-25 18:59:24,570] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:59:24,613] [INFO] Task started: CheckM
[2024-01-25 18:59:24,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000498955.2_NMG01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000498955.2_NMG01_genomic.fna/checkm_input GCF_000498955.2_NMG01_genomic.fna/checkm_result
[2024-01-25 18:59:48,067] [INFO] Task succeeded: CheckM
[2024-01-25 18:59:48,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:59:48,090] [INFO] ===== Completeness check finished =====
[2024-01-25 18:59:48,090] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:59:48,090] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000498955.2_NMG01_genomic.fna/markers.fasta)
[2024-01-25 18:59:48,090] [INFO] Task started: Blastn
[2024-01-25 18:59:48,090] [INFO] Running command: blastn -query GCF_000498955.2_NMG01_genomic.fna/markers.fasta -db /var/lib/cwl/stgdca46cd0-0b91-48ea-865c-44bf4bb5b748/dqc_reference/reference_markers_gtdb.fasta -out GCF_000498955.2_NMG01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:59:48,847] [INFO] Task succeeded: Blastn
[2024-01-25 18:59:48,850] [INFO] Selected 16 target genomes.
[2024-01-25 18:59:48,850] [INFO] Target genome list was writen to GCF_000498955.2_NMG01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:59:48,859] [INFO] Task started: fastANI
[2024-01-25 18:59:48,860] [INFO] Running command: fastANI --query /var/lib/cwl/stg037e8617-f3c5-47b6-9df8-371af8397810/GCF_000498955.2_NMG01_genomic.fna.gz --refList GCF_000498955.2_NMG01_genomic.fna/target_genomes_gtdb.txt --output GCF_000498955.2_NMG01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:59:58,099] [INFO] Task succeeded: fastANI
[2024-01-25 18:59:58,107] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:59:58,107] [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_000498955.2	s__Lactiplantibacillus fabifermentans	100.0	1002	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	conclusive
GCF_005405105.1	s__Lactiplantibacillus dongliensis	80.5044	387	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	80.4918	405	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405065.1	s__Lactiplantibacillus nangangensis	80.4666	413	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405005.1	s__Lactiplantibacillus daoliensis	80.4315	388	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405125.1	s__Lactiplantibacillus songbeiensis	80.3949	380	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405385.1	s__Lactiplantibacillus mudanjiangensis	80.1857	390	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.38	99.14	0.94	0.91	5	-
GCF_005404945.1	s__Lactiplantibacillus pingfangensis	80.1252	393	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001438845.1	s__Lactiplantibacillus xiangfangensis	80.1221	388	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	80.0629	365	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_003885105.1	s__Lactiplantibacillus garii	79.9108	353	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970915.1	s__Lactiplantibacillus sp002970915	79.8609	350	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405425.1	s__Lactiplantibacillus modestisalitolerans	79.6219	290	1010	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:59:58,110] [INFO] GTDB search result was written to GCF_000498955.2_NMG01_genomic.fna/result_gtdb.tsv
[2024-01-25 18:59:58,111] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:59:58,113] [INFO] DFAST_QC result json was written to GCF_000498955.2_NMG01_genomic.fna/dqc_result.json
[2024-01-25 18:59:58,114] [INFO] DFAST_QC completed!
[2024-01-25 18:59:58,114] [INFO] Total running time: 0h0m52s