[2024-01-25 20:05:20,532] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:20,533] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:20,533] [INFO] DQC Reference Directory: /var/lib/cwl/stg1c38430a-800f-4732-a64a-e547ca14026a/dqc_reference
[2024-01-25 20:05:21,689] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:21,689] [INFO] Task started: Prodigal
[2024-01-25 20:05:21,690] [INFO] Running command: gunzip -c /var/lib/cwl/stgd2712af9-a52a-4016-a848-f315384c03cc/GCF_001908415.1_ASM190841v1_genomic.fna.gz | prodigal -d GCF_001908415.1_ASM190841v1_genomic.fna/cds.fna -a GCF_001908415.1_ASM190841v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:26,292] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:26,292] [INFO] Task started: HMMsearch
[2024-01-25 20:05:26,292] [INFO] Running command: hmmsearch --tblout GCF_001908415.1_ASM190841v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1c38430a-800f-4732-a64a-e547ca14026a/dqc_reference/reference_markers.hmm GCF_001908415.1_ASM190841v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:26,474] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:26,475] [INFO] Found 6/6 markers.
[2024-01-25 20:05:26,493] [INFO] Query marker FASTA was written to GCF_001908415.1_ASM190841v1_genomic.fna/markers.fasta
[2024-01-25 20:05:26,493] [INFO] Task started: Blastn
[2024-01-25 20:05:26,493] [INFO] Running command: blastn -query GCF_001908415.1_ASM190841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c38430a-800f-4732-a64a-e547ca14026a/dqc_reference/reference_markers.fasta -out GCF_001908415.1_ASM190841v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:27,031] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:27,034] [INFO] Selected 11 target genomes.
[2024-01-25 20:05:27,034] [INFO] Target genome list was writen to GCF_001908415.1_ASM190841v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:27,045] [INFO] Task started: fastANI
[2024-01-25 20:05:27,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2712af9-a52a-4016-a848-f315384c03cc/GCF_001908415.1_ASM190841v1_genomic.fna.gz --refList GCF_001908415.1_ASM190841v1_genomic.fna/target_genomes.txt --output GCF_001908415.1_ASM190841v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:32,848] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:32,849] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1c38430a-800f-4732-a64a-e547ca14026a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:32,849] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1c38430a-800f-4732-a64a-e547ca14026a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:32,856] [INFO] Found 9 fastANI hits (9 hits with ANI > threshold)
[2024-01-25 20:05:32,856] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:32,856] [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
Lactobacillus delbrueckii subsp. indicus	strain=JCM 15610	GCA_001908415.1	249265	1584	type	True	100.0	667	672	95	conclusive
Lactobacillus delbrueckii subsp. indicus	strain=JCM 15610	GCA_001189855.1	249265	1584	type	True	99.8941	583	672	95	conclusive
Lactobacillus delbrueckii subsp. indicus	strain=DSM 15996	GCA_001435795.1	249265	1584	type	True	99.8546	574	672	95	conclusive
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001888965.1	1050107	1584	suspected-type	True	97.1262	545	672	95	conclusive
Lactobacillus delbrueckii subsp. sunkii	strain=JCM 17838	GCA_001190005.1	1050107	1584	suspected-type	True	97.0981	518	672	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=ATCC 11842	GCA_000056065.1	1585	1584	type	True	96.9068	550	672	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=DSM 20081	GCA_001437195.1	1585	1584	type	True	96.8579	513	672	95	conclusive
Lactobacillus delbrueckii subsp. bulgaricus	strain=NBRC 13953	GCA_006539405.1	1585	1584	type	True	96.8571	500	672	95	conclusive
Lactobacillus delbrueckii subsp. delbrueckii	strain=DSM 20074	GCA_001433875.1	83684	1584	suspected-type	True	96.5578	460	672	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:05:32,858] [INFO] DFAST Taxonomy check result was written to GCF_001908415.1_ASM190841v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:32,858] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:32,858] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:32,858] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1c38430a-800f-4732-a64a-e547ca14026a/dqc_reference/checkm_data
[2024-01-25 20:05:32,859] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:32,882] [INFO] Task started: CheckM
[2024-01-25 20:05:32,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001908415.1_ASM190841v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001908415.1_ASM190841v1_genomic.fna/checkm_input GCF_001908415.1_ASM190841v1_genomic.fna/checkm_result
[2024-01-25 20:05:52,229] [INFO] Task succeeded: CheckM
[2024-01-25 20:05:52,230] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:05:52,245] [INFO] ===== Completeness check finished =====
[2024-01-25 20:05:52,245] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:05:52,245] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001908415.1_ASM190841v1_genomic.fna/markers.fasta)
[2024-01-25 20:05:52,245] [INFO] Task started: Blastn
[2024-01-25 20:05:52,246] [INFO] Running command: blastn -query GCF_001908415.1_ASM190841v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1c38430a-800f-4732-a64a-e547ca14026a/dqc_reference/reference_markers_gtdb.fasta -out GCF_001908415.1_ASM190841v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:53,054] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:53,056] [INFO] Selected 9 target genomes.
[2024-01-25 20:05:53,057] [INFO] Target genome list was writen to GCF_001908415.1_ASM190841v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:05:53,064] [INFO] Task started: fastANI
[2024-01-25 20:05:53,064] [INFO] Running command: fastANI --query /var/lib/cwl/stgd2712af9-a52a-4016-a848-f315384c03cc/GCF_001908415.1_ASM190841v1_genomic.fna.gz --refList GCF_001908415.1_ASM190841v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001908415.1_ASM190841v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:05:57,131] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:57,136] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:05:57,136] [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_001433875.1	s__Lactobacillus delbrueckii	96.5578	460	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.56	96.59	0.89	0.81	103	conclusive
GCA_004556255.1	s__Lactobacillus delbrueckii_B	94.3371	334	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016587775.1	s__Lactobacillus nasalidis	86.7588	350	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.92	99.91	0.92	0.89	3	-
GCF_009695985.1	s__Lactobacillus porci	82.5266	395	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	97.72	97.20	0.91	0.90	4	-
GCF_001434815.1	s__Lactobacillus equicursoris	82.2325	367	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	98.84	97.67	0.88	0.82	5	-
GCF_000615445.1	s__Lactobacillus hamsteri	78.692	53	672	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Lactobacillus	95.0	99.97	99.97	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:05:57,137] [INFO] GTDB search result was written to GCF_001908415.1_ASM190841v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:05:57,138] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:05:57,140] [INFO] DFAST_QC result json was written to GCF_001908415.1_ASM190841v1_genomic.fna/dqc_result.json
[2024-01-25 20:05:57,140] [INFO] DFAST_QC completed!
[2024-01-25 20:05:57,140] [INFO] Total running time: 0h0m37s