[2024-01-24 15:26:50,853] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:50,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:50,856] [INFO] DQC Reference Directory: /var/lib/cwl/stgdeef9ad9-b241-4794-a138-fed949869ba6/dqc_reference
[2024-01-24 15:26:52,908] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:52,909] [INFO] Task started: Prodigal
[2024-01-24 15:26:52,909] [INFO] Running command: gunzip -c /var/lib/cwl/stgf37acac9-4f8d-4027-bceb-9804178bbe17/GCF_001039045.1_ASM103904v1_genomic.fna.gz | prodigal -d GCF_001039045.1_ASM103904v1_genomic.fna/cds.fna -a GCF_001039045.1_ASM103904v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:59,094] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:59,095] [INFO] Task started: HMMsearch
[2024-01-24 15:26:59,095] [INFO] Running command: hmmsearch --tblout GCF_001039045.1_ASM103904v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdeef9ad9-b241-4794-a138-fed949869ba6/dqc_reference/reference_markers.hmm GCF_001039045.1_ASM103904v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:59,359] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:59,360] [INFO] Found 6/6 markers.
[2024-01-24 15:26:59,393] [INFO] Query marker FASTA was written to GCF_001039045.1_ASM103904v1_genomic.fna/markers.fasta
[2024-01-24 15:26:59,393] [INFO] Task started: Blastn
[2024-01-24 15:26:59,393] [INFO] Running command: blastn -query GCF_001039045.1_ASM103904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeef9ad9-b241-4794-a138-fed949869ba6/dqc_reference/reference_markers.fasta -out GCF_001039045.1_ASM103904v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:00,531] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:00,535] [INFO] Selected 21 target genomes.
[2024-01-24 15:27:00,535] [INFO] Target genome list was writen to GCF_001039045.1_ASM103904v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:00,574] [INFO] Task started: fastANI
[2024-01-24 15:27:00,575] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37acac9-4f8d-4027-bceb-9804178bbe17/GCF_001039045.1_ASM103904v1_genomic.fna.gz --refList GCF_001039045.1_ASM103904v1_genomic.fna/target_genomes.txt --output GCF_001039045.1_ASM103904v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:12,806] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:12,806] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdeef9ad9-b241-4794-a138-fed949869ba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:12,806] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdeef9ad9-b241-4794-a138-fed949869ba6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:12,819] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:12,819] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:12,819] [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 herbarum	strain=TCF032-E4	GCA_001039045.1	1670446	1670446	type	True	100.0	933	937	95	conclusive
Lactiplantibacillus paraplantarum	strain=DSM 10667	GCA_003641145.1	60520	60520	type	True	81.2459	475	937	95	below_threshold
Lactiplantibacillus paraplantarum	strain=DSM 10667	GCA_001435655.1	60520	60520	type	True	81.0576	470	937	95	below_threshold
Lactiplantibacillus plantarum subsp. plantarum	strain=CGMCC 1.2437	GCA_001434175.1	337330	1590	type	True	80.9688	459	937	95	below_threshold
Lactiplantibacillus plantarum subsp. plantarum	strain=NBRC 15891	GCA_007989145.1	337330	1590	type	True	80.9068	458	937	95	below_threshold
Lactiplantibacillus plantarum	strain=DSM 20174	GCA_014131735.1	1590	1590	type	True	80.852	460	937	95	below_threshold
Lactiplantibacillus plantarum subsp. plantarum	strain=ATCC 14917	GCA_000143745.1	337330	1590	type	True	80.8169	457	937	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_003641185.1	1589	1589	type	True	80.5261	456	937	95	below_threshold
Lactiplantibacillus pentosus	strain=DSM 20314	GCA_001433755.1	1589	1589	type	True	80.5218	447	937	95	below_threshold
Lactiplantibacillus pentosus	strain=ATCC 8041	GCA_004354685.1	1589	1589	type	True	80.5125	461	937	95	below_threshold
Lactiplantibacillus xiangfangensis	strain=LMG 26013	GCA_001438845.1	942150	942150	type	True	80.1399	360	937	95	below_threshold
Lactiplantibacillus fabifermentans	strain=DSM 21115	GCA_000498955.2	483011	483011	type	True	79.7759	333	937	95	below_threshold
Lactiplantibacillus daowaiensis	strain=203-3	GCA_005405085.1	2559918	2559918	type	True	79.5576	302	937	95	below_threshold
Lactiplantibacillus songbeiensis	strain=398-2	GCA_005405125.1	2559920	2559920	type	True	79.3322	304	937	95	below_threshold
Lactiplantibacillus dongliensis	strain=218-3	GCA_005405105.1	2559919	2559919	type	True	79.2288	299	937	95	below_threshold
Secundilactobacillus pentosiphilus	strain=IWT25	GCA_002217985.1	1714682	1714682	type	True	77.622	55	937	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:12,824] [INFO] DFAST Taxonomy check result was written to GCF_001039045.1_ASM103904v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:12,824] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:12,824] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:12,825] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdeef9ad9-b241-4794-a138-fed949869ba6/dqc_reference/checkm_data
[2024-01-24 15:27:12,825] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:12,854] [INFO] Task started: CheckM
[2024-01-24 15:27:12,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001039045.1_ASM103904v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001039045.1_ASM103904v1_genomic.fna/checkm_input GCF_001039045.1_ASM103904v1_genomic.fna/checkm_result
[2024-01-24 15:27:37,128] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:37,129] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:37,147] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:37,148] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:37,148] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001039045.1_ASM103904v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:37,148] [INFO] Task started: Blastn
[2024-01-24 15:27:37,148] [INFO] Running command: blastn -query GCF_001039045.1_ASM103904v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdeef9ad9-b241-4794-a138-fed949869ba6/dqc_reference/reference_markers_gtdb.fasta -out GCF_001039045.1_ASM103904v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:37,947] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:37,951] [INFO] Selected 16 target genomes.
[2024-01-24 15:27:37,951] [INFO] Target genome list was writen to GCF_001039045.1_ASM103904v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:37,960] [INFO] Task started: fastANI
[2024-01-24 15:27:37,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgf37acac9-4f8d-4027-bceb-9804178bbe17/GCF_001039045.1_ASM103904v1_genomic.fna.gz --refList GCF_001039045.1_ASM103904v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001039045.1_ASM103904v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:47,471] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:47,484] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:47,484] [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_001039045.1	s__Lactiplantibacillus herbarum	100.0	933	937	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_003641145.1	s__Lactiplantibacillus paraplantarum	81.2319	476	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.82	97.28	0.92	0.86	13	-
GCF_014131735.1	s__Lactiplantibacillus plantarum	80.852	460	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	98.89	95.74	0.92	0.82	629	-
GCF_003641185.1	s__Lactiplantibacillus pentosus	80.5261	456	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	97.89	96.07	0.90	0.86	56	-
GCF_000463075.2	s__Lactiplantibacillus plantarum_A	80.3427	446	937	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	80.2498	329	937	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	80.156	359	937	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	79.7837	334	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	99.67	99.67	0.93	0.93	2	-
GCF_005405085.1	s__Lactiplantibacillus daowaiensis	79.5913	300	937	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	79.3969	321	937	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	79.3322	304	937	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	79.277	296	937	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	79.1154	291	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactiplantibacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002217985.1	s__Secundilactobacillus pentosiphilus	77.5651	56	937	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.11	97.11	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:47,486] [INFO] GTDB search result was written to GCF_001039045.1_ASM103904v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:47,487] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:47,490] [INFO] DFAST_QC result json was written to GCF_001039045.1_ASM103904v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:47,490] [INFO] DFAST_QC completed!
[2024-01-24 15:27:47,491] [INFO] Total running time: 0h0m57s