[2024-01-24 11:59:51,989] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:51,991] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:51,991] [INFO] DQC Reference Directory: /var/lib/cwl/stgcc06d912-1464-4a31-9945-129fee9ae1c2/dqc_reference
[2024-01-24 11:59:55,381] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:55,382] [INFO] Task started: Prodigal
[2024-01-24 11:59:55,383] [INFO] Running command: gunzip -c /var/lib/cwl/stgbb15c37f-0923-458c-9ab2-770ada60fbeb/GCF_024160875.1_ASM2416087v1_genomic.fna.gz | prodigal -d GCF_024160875.1_ASM2416087v1_genomic.fna/cds.fna -a GCF_024160875.1_ASM2416087v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:00:00,028] [INFO] Task succeeded: Prodigal
[2024-01-24 12:00:00,028] [INFO] Task started: HMMsearch
[2024-01-24 12:00:00,028] [INFO] Running command: hmmsearch --tblout GCF_024160875.1_ASM2416087v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcc06d912-1464-4a31-9945-129fee9ae1c2/dqc_reference/reference_markers.hmm GCF_024160875.1_ASM2416087v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:00:00,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:00:00,273] [INFO] Found 6/6 markers.
[2024-01-24 12:00:00,296] [INFO] Query marker FASTA was written to GCF_024160875.1_ASM2416087v1_genomic.fna/markers.fasta
[2024-01-24 12:00:00,296] [INFO] Task started: Blastn
[2024-01-24 12:00:00,297] [INFO] Running command: blastn -query GCF_024160875.1_ASM2416087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc06d912-1464-4a31-9945-129fee9ae1c2/dqc_reference/reference_markers.fasta -out GCF_024160875.1_ASM2416087v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:01,466] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:01,470] [INFO] Selected 30 target genomes.
[2024-01-24 12:00:01,471] [INFO] Target genome list was writen to GCF_024160875.1_ASM2416087v1_genomic.fna/target_genomes.txt
[2024-01-24 12:00:01,570] [INFO] Task started: fastANI
[2024-01-24 12:00:01,570] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb15c37f-0923-458c-9ab2-770ada60fbeb/GCF_024160875.1_ASM2416087v1_genomic.fna.gz --refList GCF_024160875.1_ASM2416087v1_genomic.fna/target_genomes.txt --output GCF_024160875.1_ASM2416087v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:00:12,343] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:12,344] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcc06d912-1464-4a31-9945-129fee9ae1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:00:12,345] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcc06d912-1464-4a31-9945-129fee9ae1c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:00:12,365] [INFO] Found 18 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:00:12,365] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:00:12,365] [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
Ligilactobacillus agilis	strain=DSM 20509	GCA_001436215.1	1601	1601	type	True	78.584	103	834	95	below_threshold
Ligilactobacillus animalis	strain=KCTC 3501	GCA_000183825.1	1605	1605	type	True	78.5035	53	834	95	below_threshold
Ligilactobacillus animalis	strain=DSM 20602	GCA_001434535.1	1605	1605	type	True	78.1588	53	834	95	below_threshold
Ligilactobacillus apodemi	strain=DSM 16634	GCA_001434405.1	307126	307126	type	True	78.1126	73	834	95	below_threshold
Ligilactobacillus apodemi	strain=JCM 16172	GCA_000615885.1	307126	307126	type	True	77.9836	73	834	95	below_threshold
Liquorilactobacillus nagelii	strain=DSM 13675	GCA_019444005.1	82688	82688	type	True	77.974	108	834	95	below_threshold
Liquorilactobacillus hordei	strain=DSM 19519	GCA_019443985.1	468911	468911	type	True	77.9137	102	834	95	below_threshold
Liquorilactobacillus nagelii	strain=DSM 13675	GCA_001434225.1	82688	82688	type	True	77.8656	101	834	95	below_threshold
Ligilactobacillus murinus	strain=DSM 20452	GCA_001436015.1	1622	1622	type	True	77.8557	73	834	95	below_threshold
Liquorilactobacillus mali	strain=KCTC 3596	GCA_000260415.1	1618	1618	type	True	77.7393	90	834	95	below_threshold
Ligilactobacillus salivarius	strain=DSM 20554	GCA_002079585.1	1624	1624	type	True	77.7321	100	834	95	below_threshold
Liquorilactobacillus hordei	strain=DSM 19519	GCA_001434845.1	468911	468911	type	True	77.702	97	834	95	below_threshold
Liquorilactobacillus mali	strain=DSM 20444	GCA_001436535.1	1618	1618	type	True	77.6515	87	834	95	below_threshold
Liquorilactobacillus oeni	strain=DSM 19972	GCA_001436275.1	303241	303241	type	True	77.3897	65	834	95	below_threshold
Ligilactobacillus pobuzihii	strain=KCTC 13174	GCA_001433815.1	449659	449659	type	True	77.372	65	834	95	below_threshold
Liquorilactobacillus uvarum	strain=DSM 19971	GCA_001434935.1	303240	303240	type	True	77.3018	90	834	95	below_threshold
Ligilactobacillus pobuzihii	strain=E100301	GCA_000349725.1	449659	449659	type	True	77.1564	66	834	95	below_threshold
Liquorilactobacillus capillatus	strain=DSM 19910	GCA_001434915.1	480931	480931	type	True	77.0581	85	834	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:00:12,367] [INFO] DFAST Taxonomy check result was written to GCF_024160875.1_ASM2416087v1_genomic.fna/tc_result.tsv
[2024-01-24 12:00:12,368] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:00:12,368] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:00:12,368] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcc06d912-1464-4a31-9945-129fee9ae1c2/dqc_reference/checkm_data
[2024-01-24 12:00:12,369] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:00:12,400] [INFO] Task started: CheckM
[2024-01-24 12:00:12,401] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024160875.1_ASM2416087v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024160875.1_ASM2416087v1_genomic.fna/checkm_input GCF_024160875.1_ASM2416087v1_genomic.fna/checkm_result
[2024-01-24 12:00:33,314] [INFO] Task succeeded: CheckM
[2024-01-24 12:00:33,315] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:00:33,338] [INFO] ===== Completeness check finished =====
[2024-01-24 12:00:33,338] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:00:33,339] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024160875.1_ASM2416087v1_genomic.fna/markers.fasta)
[2024-01-24 12:00:33,339] [INFO] Task started: Blastn
[2024-01-24 12:00:33,339] [INFO] Running command: blastn -query GCF_024160875.1_ASM2416087v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcc06d912-1464-4a31-9945-129fee9ae1c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_024160875.1_ASM2416087v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:00:34,065] [INFO] Task succeeded: Blastn
[2024-01-24 12:00:34,070] [INFO] Selected 31 target genomes.
[2024-01-24 12:00:34,071] [INFO] Target genome list was writen to GCF_024160875.1_ASM2416087v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:00:34,093] [INFO] Task started: fastANI
[2024-01-24 12:00:34,093] [INFO] Running command: fastANI --query /var/lib/cwl/stgbb15c37f-0923-458c-9ab2-770ada60fbeb/GCF_024160875.1_ASM2416087v1_genomic.fna.gz --refList GCF_024160875.1_ASM2416087v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024160875.1_ASM2416087v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:00:44,404] [INFO] Task succeeded: fastANI
[2024-01-24 12:00:44,418] [INFO] Found 18 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:00:44,418] [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_001436215.1	s__Ligilactobacillus agilis	78.584	103	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.37	95.88	0.84	0.79	29	-
GCF_001434535.1	s__Ligilactobacillus animalis	78.1588	53	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	98.99	95.79	0.93	0.90	12	-
GCF_001434405.1	s__Ligilactobacillus apodemi	78.1126	73	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	1.00	1.00	2	-
GCF_001434225.1	s__Liquorilactobacillus nagelii	77.8656	101	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.67	98.67	0.89	0.89	2	-
GCA_905204935.1	s__Ligilactobacillus sp900765635	77.7905	99	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.92	0.92	2	-
GCF_000260415.1	s__Liquorilactobacillus mali	77.7393	90	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.97	99.95	0.96	0.94	4	-
GCF_001434845.1	s__Liquorilactobacillus hordei	77.702	97	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.13	98.13	0.87	0.87	2	-
GCF_001591685.1	s__Ligilactobacillus murinus	77.7002	70	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.01	96.68	0.83	0.78	62	-
GCF_000615845.1	s__Ligilactobacillus hayakitensis	77.6193	77	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.97	99.97	0.98	0.98	2	-
GCF_900110005.1	s__Ligilactobacillus ruminis_A	77.5841	74	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.72	99.72	0.98	0.98	2	-
GCF_001435955.1	s__Ligilactobacillus salivarius	77.4926	103	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.81	97.07	0.87	0.79	193	-
GCF_001437155.1	s__Liquorilactobacillus mali_A	77.4889	90	834	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	77.397	64	834	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	77.3018	90	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000349725.1	s__Ligilactobacillus pobuzihii	77.1528	67	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.98	1.00	0.99	4	-
GCF_001434915.1	s__Liquorilactobacillus capillatus	77.0581	85	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019116985.1	s__Ligilactobacillus excrementavium	76.745	50	834	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	97.12	97.12	0.91	0.91	2	-
GCA_019114385.1	s__Ligilactobacillus excrementigallinarum	76.658	66	834	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 12:00:44,420] [INFO] GTDB search result was written to GCF_024160875.1_ASM2416087v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:00:44,420] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:00:44,425] [INFO] DFAST_QC result json was written to GCF_024160875.1_ASM2416087v1_genomic.fna/dqc_result.json
[2024-01-24 12:00:44,425] [INFO] DFAST_QC completed!
[2024-01-24 12:00:44,425] [INFO] Total running time: 0h0m52s