[2024-01-24 15:02:33,643] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:33,644] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:33,645] [INFO] DQC Reference Directory: /var/lib/cwl/stg712c489b-d19f-42d5-9c58-b0b95fcece76/dqc_reference
[2024-01-24 15:02:34,981] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:34,982] [INFO] Task started: Prodigal
[2024-01-24 15:02:34,982] [INFO] Running command: gunzip -c /var/lib/cwl/stg455728b2-44a3-40af-a21b-f3160362f14d/GCF_019443985.1_ASM1944398v1_genomic.fna.gz | prodigal -d GCF_019443985.1_ASM1944398v1_genomic.fna/cds.fna -a GCF_019443985.1_ASM1944398v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:02:39,917] [INFO] Task succeeded: Prodigal
[2024-01-24 15:02:39,918] [INFO] Task started: HMMsearch
[2024-01-24 15:02:39,918] [INFO] Running command: hmmsearch --tblout GCF_019443985.1_ASM1944398v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg712c489b-d19f-42d5-9c58-b0b95fcece76/dqc_reference/reference_markers.hmm GCF_019443985.1_ASM1944398v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:02:40,178] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:02:40,180] [INFO] Found 6/6 markers.
[2024-01-24 15:02:40,204] [INFO] Query marker FASTA was written to GCF_019443985.1_ASM1944398v1_genomic.fna/markers.fasta
[2024-01-24 15:02:40,205] [INFO] Task started: Blastn
[2024-01-24 15:02:40,205] [INFO] Running command: blastn -query GCF_019443985.1_ASM1944398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg712c489b-d19f-42d5-9c58-b0b95fcece76/dqc_reference/reference_markers.fasta -out GCF_019443985.1_ASM1944398v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:02:40,819] [INFO] Task succeeded: Blastn
[2024-01-24 15:02:40,826] [INFO] Selected 17 target genomes.
[2024-01-24 15:02:40,827] [INFO] Target genome list was writen to GCF_019443985.1_ASM1944398v1_genomic.fna/target_genomes.txt
[2024-01-24 15:02:40,839] [INFO] Task started: fastANI
[2024-01-24 15:02:40,840] [INFO] Running command: fastANI --query /var/lib/cwl/stg455728b2-44a3-40af-a21b-f3160362f14d/GCF_019443985.1_ASM1944398v1_genomic.fna.gz --refList GCF_019443985.1_ASM1944398v1_genomic.fna/target_genomes.txt --output GCF_019443985.1_ASM1944398v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:02:50,372] [INFO] Task succeeded: fastANI
[2024-01-24 15:02:50,373] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg712c489b-d19f-42d5-9c58-b0b95fcece76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:02:50,373] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg712c489b-d19f-42d5-9c58-b0b95fcece76/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:02:50,382] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:02:50,382] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:02:50,383] [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
Liquorilactobacillus hordei	strain=DSM 19519	GCA_019443985.1	468911	468911	type	True	100.0	807	812	95	conclusive
Liquorilactobacillus hordei	strain=DSM 19519	GCA_001434845.1	468911	468911	type	True	99.8751	698	812	95	conclusive
Liquorilactobacillus mali	strain=KCTC 3596	GCA_000260415.1	1618	1618	type	True	82.7626	521	812	95	below_threshold
Liquorilactobacillus mali	strain=DSM 20444	GCA_000276905.1	1618	1618	type	True	82.758	410	812	95	below_threshold
Liquorilactobacillus mali	strain=DSM 20444	GCA_001436535.1	1618	1618	type	True	82.7394	515	812	95	below_threshold
Liquorilactobacillus uvarum	strain=DSM 19971	GCA_001434935.1	303240	303240	type	True	78.7202	128	812	95	below_threshold
Liquorilactobacillus oeni	strain=DSM 19972	GCA_001436275.1	303241	303241	type	True	78.6869	113	812	95	below_threshold
Ligilactobacillus salivarius	strain=ATCC 11741	GCA_000159395.1	1624	1624	type	True	77.983	73	812	95	below_threshold
Ligilactobacillus salivarius	strain=DSM 20554	GCA_002079585.1	1624	1624	type	True	77.9343	74	812	95	below_threshold
Ligilactobacillus salivarius	strain=DSM 20555	GCA_001435955.1	1624	1624	type	True	77.8998	70	812	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:02:50,384] [INFO] DFAST Taxonomy check result was written to GCF_019443985.1_ASM1944398v1_genomic.fna/tc_result.tsv
[2024-01-24 15:02:50,385] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:02:50,385] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:02:50,385] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg712c489b-d19f-42d5-9c58-b0b95fcece76/dqc_reference/checkm_data
[2024-01-24 15:02:50,386] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:02:50,417] [INFO] Task started: CheckM
[2024-01-24 15:02:50,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019443985.1_ASM1944398v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019443985.1_ASM1944398v1_genomic.fna/checkm_input GCF_019443985.1_ASM1944398v1_genomic.fna/checkm_result
[2024-01-24 15:03:13,748] [INFO] Task succeeded: CheckM
[2024-01-24 15:03:13,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:03:13,795] [INFO] ===== Completeness check finished =====
[2024-01-24 15:03:13,796] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:03:13,796] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019443985.1_ASM1944398v1_genomic.fna/markers.fasta)
[2024-01-24 15:03:13,797] [INFO] Task started: Blastn
[2024-01-24 15:03:13,797] [INFO] Running command: blastn -query GCF_019443985.1_ASM1944398v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg712c489b-d19f-42d5-9c58-b0b95fcece76/dqc_reference/reference_markers_gtdb.fasta -out GCF_019443985.1_ASM1944398v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:14,621] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:14,625] [INFO] Selected 18 target genomes.
[2024-01-24 15:03:14,625] [INFO] Target genome list was writen to GCF_019443985.1_ASM1944398v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:03:14,637] [INFO] Task started: fastANI
[2024-01-24 15:03:14,638] [INFO] Running command: fastANI --query /var/lib/cwl/stg455728b2-44a3-40af-a21b-f3160362f14d/GCF_019443985.1_ASM1944398v1_genomic.fna.gz --refList GCF_019443985.1_ASM1944398v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019443985.1_ASM1944398v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:03:24,618] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:24,627] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:03:24,628] [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_001434845.1	s__Liquorilactobacillus hordei	99.8751	698	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.13	98.13	0.87	0.87	2	conclusive
GCF_000260415.1	s__Liquorilactobacillus mali	82.7441	521	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.97	99.95	0.96	0.94	4	-
GCF_001437155.1	s__Liquorilactobacillus mali_A	82.7219	533	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436735.1	s__Liquorilactobacillus cacaonum	80.4146	326	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001436275.1	s__Liquorilactobacillus oeni	78.6867	113	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001434935.1	s__Liquorilactobacillus uvarum	78.644	132	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000255495.1	s__Liquorilactobacillus vini	77.9196	82	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.24	98.67	0.86	0.83	3	-
GCF_001435955.1	s__Ligilactobacillus salivarius	77.8998	70	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.81	97.07	0.87	0.79	193	-
GCF_001434225.1	s__Liquorilactobacillus nagelii	77.6764	127	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.67	98.67	0.89	0.89	2	-
GCA_019114385.1	s__Ligilactobacillus excrementigallinarum	76.1811	53	812	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:03:24,630] [INFO] GTDB search result was written to GCF_019443985.1_ASM1944398v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:03:24,631] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:03:24,636] [INFO] DFAST_QC result json was written to GCF_019443985.1_ASM1944398v1_genomic.fna/dqc_result.json
[2024-01-24 15:03:24,637] [INFO] DFAST_QC completed!
[2024-01-24 15:03:24,637] [INFO] Total running time: 0h0m51s