[2024-01-24 13:57:00,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:00,645] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:00,646] [INFO] DQC Reference Directory: /var/lib/cwl/stga421b750-3024-44d6-9e7f-c76b620384e0/dqc_reference
[2024-01-24 13:57:02,047] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:02,048] [INFO] Task started: Prodigal
[2024-01-24 13:57:02,048] [INFO] Running command: gunzip -c /var/lib/cwl/stg4aa67f9e-2807-4aaf-b385-ca5088f07acf/GCF_005405085.1_ASM540508v1_genomic.fna.gz | prodigal -d GCF_005405085.1_ASM540508v1_genomic.fna/cds.fna -a GCF_005405085.1_ASM540508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:08,865] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:08,865] [INFO] Task started: HMMsearch
[2024-01-24 13:57:08,866] [INFO] Running command: hmmsearch --tblout GCF_005405085.1_ASM540508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga421b750-3024-44d6-9e7f-c76b620384e0/dqc_reference/reference_markers.hmm GCF_005405085.1_ASM540508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:09,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:09,156] [INFO] Found 6/6 markers.
[2024-01-24 13:57:09,187] [INFO] Query marker FASTA was written to GCF_005405085.1_ASM540508v1_genomic.fna/markers.fasta
[2024-01-24 13:57:09,187] [INFO] Task started: Blastn
[2024-01-24 13:57:09,187] [INFO] Running command: blastn -query GCF_005405085.1_ASM540508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga421b750-3024-44d6-9e7f-c76b620384e0/dqc_reference/reference_markers.fasta -out GCF_005405085.1_ASM540508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:09,848] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:09,853] [INFO] Selected 18 target genomes.
[2024-01-24 13:57:09,853] [INFO] Target genome list was writen to GCF_005405085.1_ASM540508v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:09,870] [INFO] Task started: fastANI
[2024-01-24 13:57:09,870] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa67f9e-2807-4aaf-b385-ca5088f07acf/GCF_005405085.1_ASM540508v1_genomic.fna.gz --refList GCF_005405085.1_ASM540508v1_genomic.fna/target_genomes.txt --output GCF_005405085.1_ASM540508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:57:19,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:19,315] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga421b750-3024-44d6-9e7f-c76b620384e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:57:19,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga421b750-3024-44d6-9e7f-c76b620384e0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:57:19,329] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:57:19,329] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:57:19,330] [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 daowaiensis	strain=203-3	GCA_005405085.1	2559918	2559918	type	True	100.0	925	931	95	conclusive
Lactiplantibacillus mudanjiangensis	strain=11050	GCA_005405385.1	1296538	1296538	type	True	82.0299	561	931	95	below_threshold
Lactiplantibacillus songbeiensis	strain=398-2	GCA_005405125.1	2559920	2559920	type	True	81.2151	491	931	95	below_threshold
Lactiplantibacillus dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	81.0429	486	931	95	below_threshold
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	80.6851	407	931	95	below_threshold
Lactiplantibacillus nangangensis	strain=381-7	GCA_005405065.1	2559917	2559917	type	True	80.5904	385	931	95	below_threshold
Lactiplantibacillus daoliensis	strain=116-1A	GCA_005405005.1	2559916	2559916	type	True	80.4568	362	931	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	80.2583	313	931	95	below_threshold
Lactiplantibacillus xiangfangensis	strain=LMG 26013	GCA_001438845.1	942150	942150	type	True	80.2094	319	931	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	80.1859	315	931	95	below_threshold
Lactiplantibacillus modestisalitolerans	strain=NBRC 107235	GCA_005405425.1	1457219	1457219	type	True	79.692	257	931	95	below_threshold
Secundilactobacillus odoratitofui	strain=JCM 15043	GCA_001313185.1	480930	480930	type	True	78.1711	68	931	95	below_threshold
Secundilactobacillus mixtipabuli	strain=IWT30	GCA_002217925.1	1435342	1435342	type	True	78.0374	61	931	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:57:19,332] [INFO] DFAST Taxonomy check result was written to GCF_005405085.1_ASM540508v1_genomic.fna/tc_result.tsv
[2024-01-24 13:57:19,332] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:57:19,332] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:57:19,333] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga421b750-3024-44d6-9e7f-c76b620384e0/dqc_reference/checkm_data
[2024-01-24 13:57:19,334] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:57:19,362] [INFO] Task started: CheckM
[2024-01-24 13:57:19,363] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005405085.1_ASM540508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005405085.1_ASM540508v1_genomic.fna/checkm_input GCF_005405085.1_ASM540508v1_genomic.fna/checkm_result
[2024-01-24 13:57:45,933] [INFO] Task succeeded: CheckM
[2024-01-24 13:57:45,934] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:57:45,954] [INFO] ===== Completeness check finished =====
[2024-01-24 13:57:45,954] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:57:45,955] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005405085.1_ASM540508v1_genomic.fna/markers.fasta)
[2024-01-24 13:57:45,955] [INFO] Task started: Blastn
[2024-01-24 13:57:45,955] [INFO] Running command: blastn -query GCF_005405085.1_ASM540508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga421b750-3024-44d6-9e7f-c76b620384e0/dqc_reference/reference_markers_gtdb.fasta -out GCF_005405085.1_ASM540508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:46,795] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:46,800] [INFO] Selected 14 target genomes.
[2024-01-24 13:57:46,800] [INFO] Target genome list was writen to GCF_005405085.1_ASM540508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:57:46,811] [INFO] Task started: fastANI
[2024-01-24 13:57:46,811] [INFO] Running command: fastANI --query /var/lib/cwl/stg4aa67f9e-2807-4aaf-b385-ca5088f07acf/GCF_005405085.1_ASM540508v1_genomic.fna.gz --refList GCF_005405085.1_ASM540508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005405085.1_ASM540508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:57:54,514] [INFO] Task succeeded: fastANI
[2024-01-24 13:57:54,525] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:57:54,525] [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_005405085.1	s__Lactiplantibacillus daowaiensis	100.0	925	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_005405385.1	s__Lactiplantibacillus mudanjiangensis	82.0169	562	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.38	99.14	0.94	0.91	5	-
GCF_005405125.1	s__Lactiplantibacillus songbeiensis	81.2017	492	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405105.1	s__Lactiplantibacillus dongliensis	81.0429	486	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000498955.2	s__Lactiplantibacillus fabifermentans	80.7158	405	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_005405065.1	s__Lactiplantibacillus nangangensis	80.5589	387	931	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	80.4563	362	931	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	80.2268	318	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002970935.1	s__Lactiplantibacillus sp002970935	80.2142	359	931	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	80.2129	341	931	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	80.0643	320	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.70	97.70	0.91	0.91	2	-
GCF_005405425.1	s__Lactiplantibacillus modestisalitolerans	79.692	257	931	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:57:54,526] [INFO] GTDB search result was written to GCF_005405085.1_ASM540508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:57:54,527] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:57:54,530] [INFO] DFAST_QC result json was written to GCF_005405085.1_ASM540508v1_genomic.fna/dqc_result.json
[2024-01-24 13:57:54,530] [INFO] DFAST_QC completed!
[2024-01-24 13:57:54,530] [INFO] Total running time: 0h0m54s