[2024-01-25 19:57:05,627] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:57:05,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:57:05,629] [INFO] DQC Reference Directory: /var/lib/cwl/stg56b733e3-7e9e-4d85-a40d-840717892062/dqc_reference
[2024-01-25 19:57:06,747] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:57:06,747] [INFO] Task started: Prodigal
[2024-01-25 19:57:06,748] [INFO] Running command: gunzip -c /var/lib/cwl/stg0171daeb-55b7-4fdc-8c16-89419b245b42/GCF_001313205.1_ASM131320v1_genomic.fna.gz | prodigal -d GCF_001313205.1_ASM131320v1_genomic.fna/cds.fna -a GCF_001313205.1_ASM131320v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:57:12,288] [INFO] Task succeeded: Prodigal
[2024-01-25 19:57:12,288] [INFO] Task started: HMMsearch
[2024-01-25 19:57:12,288] [INFO] Running command: hmmsearch --tblout GCF_001313205.1_ASM131320v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg56b733e3-7e9e-4d85-a40d-840717892062/dqc_reference/reference_markers.hmm GCF_001313205.1_ASM131320v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:57:12,483] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:57:12,484] [INFO] Found 6/6 markers.
[2024-01-25 19:57:12,508] [INFO] Query marker FASTA was written to GCF_001313205.1_ASM131320v1_genomic.fna/markers.fasta
[2024-01-25 19:57:12,509] [INFO] Task started: Blastn
[2024-01-25 19:57:12,509] [INFO] Running command: blastn -query GCF_001313205.1_ASM131320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56b733e3-7e9e-4d85-a40d-840717892062/dqc_reference/reference_markers.fasta -out GCF_001313205.1_ASM131320v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:13,085] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:13,088] [INFO] Selected 29 target genomes.
[2024-01-25 19:57:13,088] [INFO] Target genome list was writen to GCF_001313205.1_ASM131320v1_genomic.fna/target_genomes.txt
[2024-01-25 19:57:13,107] [INFO] Task started: fastANI
[2024-01-25 19:57:13,107] [INFO] Running command: fastANI --query /var/lib/cwl/stg0171daeb-55b7-4fdc-8c16-89419b245b42/GCF_001313205.1_ASM131320v1_genomic.fna.gz --refList GCF_001313205.1_ASM131320v1_genomic.fna/target_genomes.txt --output GCF_001313205.1_ASM131320v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:57:25,965] [INFO] Task succeeded: fastANI
[2024-01-25 19:57:25,965] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg56b733e3-7e9e-4d85-a40d-840717892062/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:57:25,965] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg56b733e3-7e9e-4d85-a40d-840717892062/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:57:25,975] [INFO] Found 16 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:57:25,976] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:57:25,976] [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
Secundilactobacillus kimchicus	strain=JCM 15530	GCA_001433995.1	528209	528209	type	True	99.8211	845	852	95	conclusive
Levilactobacillus zymae	strain=DSM 19395	GCA_001434115.1	267363	267363	type	True	78.533	51	852	95	below_threshold
Secundilactobacillus odoratitofui	strain=DSM 19909	GCA_001434895.1	480930	480930	type	True	78.4447	127	852	95	below_threshold
Secundilactobacillus odoratitofui	strain=JCM 15043	GCA_001313185.1	480930	480930	type	True	78.39	130	852	95	below_threshold
Levilactobacillus brevis	strain=DSM 20054	GCA_001433855.1	1580	1580	type	True	78.3833	56	852	95	below_threshold
Levilactobacillus brevis	strain=ATCC 14869	GCA_000469365.1	1580	1580	type	True	78.3668	56	852	95	below_threshold
Levilactobacillus brevis	strain=NCTC13768	GCA_900475625.1	1580	1580	type	True	78.3469	59	852	95	below_threshold
Secundilactobacillus similis	strain=DSM 23365	GCA_001436595.1	414682	414682	type	True	78.1684	134	852	95	below_threshold
Secundilactobacillus similis	strain=JCM 2765	GCA_001311075.1	414682	414682	type	True	78.1602	127	852	95	below_threshold
Secundilactobacillus collinoides	strain=JCM 1123	GCA_001312845.1	33960	33960	type	True	78.0017	118	852	95	below_threshold
Secundilactobacillus silagincola	strain=IWT5	GCA_002583405.1	1714681	1714681	type	True	77.9869	105	852	95	below_threshold
Secundilactobacillus silagei	strain=DSM 27022	GCA_004354595.1	1293415	1293415	type	True	77.9457	112	852	95	below_threshold
Levilactobacillus mulengensis	strain=112-3	GCA_003946045.1	2486025	2486025	type	True	77.9416	51	852	95	below_threshold
Secundilactobacillus silagei	strain=IWT126	GCA_002217945.1	1293415	1293415	type	True	77.809	109	852	95	below_threshold
Secundilactobacillus angelensis	strain=HBUAS51383	GCA_012641075.1	2722706	2722706	type	True	77.7685	117	852	95	below_threshold
Secundilactobacillus hailunensis	strain=887-11	GCA_005405185.1	2559923	2559923	type	True	77.6758	113	852	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:57:25,977] [INFO] DFAST Taxonomy check result was written to GCF_001313205.1_ASM131320v1_genomic.fna/tc_result.tsv
[2024-01-25 19:57:25,978] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:57:25,978] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:57:25,978] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg56b733e3-7e9e-4d85-a40d-840717892062/dqc_reference/checkm_data
[2024-01-25 19:57:25,979] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:57:26,009] [INFO] Task started: CheckM
[2024-01-25 19:57:26,009] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001313205.1_ASM131320v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001313205.1_ASM131320v1_genomic.fna/checkm_input GCF_001313205.1_ASM131320v1_genomic.fna/checkm_result
[2024-01-25 19:57:47,970] [INFO] Task succeeded: CheckM
[2024-01-25 19:57:47,971] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:57:47,987] [INFO] ===== Completeness check finished =====
[2024-01-25 19:57:47,987] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:57:47,987] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001313205.1_ASM131320v1_genomic.fna/markers.fasta)
[2024-01-25 19:57:47,987] [INFO] Task started: Blastn
[2024-01-25 19:57:47,988] [INFO] Running command: blastn -query GCF_001313205.1_ASM131320v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg56b733e3-7e9e-4d85-a40d-840717892062/dqc_reference/reference_markers_gtdb.fasta -out GCF_001313205.1_ASM131320v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:57:48,877] [INFO] Task succeeded: Blastn
[2024-01-25 19:57:48,880] [INFO] Selected 33 target genomes.
[2024-01-25 19:57:48,880] [INFO] Target genome list was writen to GCF_001313205.1_ASM131320v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:57:48,909] [INFO] Task started: fastANI
[2024-01-25 19:57:48,910] [INFO] Running command: fastANI --query /var/lib/cwl/stg0171daeb-55b7-4fdc-8c16-89419b245b42/GCF_001313205.1_ASM131320v1_genomic.fna.gz --refList GCF_001313205.1_ASM131320v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001313205.1_ASM131320v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:58:03,651] [INFO] Task succeeded: fastANI
[2024-01-25 19:58:03,661] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:58:03,661] [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_001433995.1	s__Secundilactobacillus kimchicus	99.8211	845	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.61	99.40	0.97	0.95	3	conclusive
GCF_001434115.1	s__Levilactobacillus zymae	78.533	51	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.08	97.26	0.95	0.86	4	-
GCF_001434895.1	s__Secundilactobacillus odoratitofui	78.4496	127	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.87	99.87	1.00	1.00	2	-
GCF_001433855.1	s__Levilactobacillus brevis	78.3833	56	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	97.91	96.65	0.91	0.84	85	-
GCF_001311135.1	s__Secundilactobacillus paracollinoides	78.369	107	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.57	99.45	0.95	0.89	5	-
GCF_001311075.1	s__Secundilactobacillus similis	78.1602	127	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.93	99.93	0.98	0.98	2	-
GCF_001435095.1	s__Levilactobacillus spicheri	78.0978	53	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	98.77	97.54	0.95	0.91	3	-
GCF_002583405.1	s__Secundilactobacillus silagincola	77.9869	105	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	97.58	97.58	0.87	0.87	2	-
GCF_007115095.1	s__Levilactobacillus enshiensis	77.9622	55	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946045.1	s__Levilactobacillus mulengensis	77.9416	51	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745505.1	s__Levilactobacillus suantsaiihabitans	77.859	58	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001435975.1	s__Secundilactobacillus collinoides	77.8529	119	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.82	99.79	0.97	0.94	3	-
GCF_002217945.1	s__Secundilactobacillus silagei	77.809	109	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	99.92	99.86	1.00	0.99	3	-
GCF_012641075.1	s__Secundilactobacillus sp012641075	77.7685	117	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003946085.1	s__Levilactobacillus angrenensis	77.6889	62	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005405185.1	s__Secundilactobacillus sp005405185	77.6758	113	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Secundilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016861585.1	s__Levilactobacillus sp016861585	77.6252	52	852	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Levilactobacillus	95.0	99.88	99.88	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:58:03,663] [INFO] GTDB search result was written to GCF_001313205.1_ASM131320v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:58:03,664] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:58:03,667] [INFO] DFAST_QC result json was written to GCF_001313205.1_ASM131320v1_genomic.fna/dqc_result.json
[2024-01-25 19:58:03,667] [INFO] DFAST_QC completed!
[2024-01-25 19:58:03,667] [INFO] Total running time: 0h0m58s