[2024-01-24 14:55:49,830] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:55:49,832] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:55:49,832] [INFO] DQC Reference Directory: /var/lib/cwl/stg4534fb43-e00d-4134-acec-2d6b3470337a/dqc_reference
[2024-01-24 14:55:51,122] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:55:51,123] [INFO] Task started: Prodigal
[2024-01-24 14:55:51,124] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2bfb12f-50d8-4f8c-abf1-d9c9ebe3401c/GCF_019444005.1_ASM1944400v1_genomic.fna.gz | prodigal -d GCF_019444005.1_ASM1944400v1_genomic.fna/cds.fna -a GCF_019444005.1_ASM1944400v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:56,367] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:56,368] [INFO] Task started: HMMsearch
[2024-01-24 14:55:56,368] [INFO] Running command: hmmsearch --tblout GCF_019444005.1_ASM1944400v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4534fb43-e00d-4134-acec-2d6b3470337a/dqc_reference/reference_markers.hmm GCF_019444005.1_ASM1944400v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:56,605] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:56,606] [INFO] Found 6/6 markers.
[2024-01-24 14:55:56,633] [INFO] Query marker FASTA was written to GCF_019444005.1_ASM1944400v1_genomic.fna/markers.fasta
[2024-01-24 14:55:56,634] [INFO] Task started: Blastn
[2024-01-24 14:55:56,634] [INFO] Running command: blastn -query GCF_019444005.1_ASM1944400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4534fb43-e00d-4134-acec-2d6b3470337a/dqc_reference/reference_markers.fasta -out GCF_019444005.1_ASM1944400v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:57,244] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:57,247] [INFO] Selected 17 target genomes.
[2024-01-24 14:55:57,247] [INFO] Target genome list was writen to GCF_019444005.1_ASM1944400v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:57,257] [INFO] Task started: fastANI
[2024-01-24 14:55:57,257] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2bfb12f-50d8-4f8c-abf1-d9c9ebe3401c/GCF_019444005.1_ASM1944400v1_genomic.fna.gz --refList GCF_019444005.1_ASM1944400v1_genomic.fna/target_genomes.txt --output GCF_019444005.1_ASM1944400v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:56:04,165] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:04,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4534fb43-e00d-4134-acec-2d6b3470337a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:56:04,166] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4534fb43-e00d-4134-acec-2d6b3470337a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:56:04,182] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:56:04,182] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:56:04,182] [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 nagelii	strain=DSM 13675	GCA_019444005.1	82688	82688	type	True	100.0	851	854	95	conclusive
Liquorilactobacillus nagelii	strain=DSM 13675	GCA_001434225.1	82688	82688	type	True	99.9518	811	854	95	conclusive
Pediococcus claussenii	strain=ATCC BAA-344	GCA_000237995.2	187452	187452	type	True	80.3317	50	854	95	below_threshold
Liquorilactobacillus ghanensis	strain=DSM 18630	GCA_001435235.1	399370	399370	type	True	80.1491	448	854	95	below_threshold
Liquorilactobacillus mali	strain=KCTC 3596	GCA_000260415.1	1618	1618	type	True	79.2045	118	854	95	below_threshold
Liquorilactobacillus vini	strain=DSM 20605	GCA_000255495.2	238015	238015	type	True	78.4394	192	854	95	below_threshold
Liquorilactobacillus vini	strain=DSM 20605	GCA_001435395.1	238015	238015	type	True	78.0952	188	854	95	below_threshold
Liquorilactobacillus sucicola	strain=DSM 21376	GCA_001436705.1	519050	519050	type	True	77.8036	100	854	95	below_threshold
Liquorilactobacillus sucicola	strain=JCM 15457	GCA_000612445.1	519050	519050	type	True	77.7113	101	854	95	below_threshold
Liquorilactobacillus cacaonum	strain=DSM 21116	GCA_001436735.1	483012	483012	type	True	77.5192	115	854	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:56:04,183] [INFO] DFAST Taxonomy check result was written to GCF_019444005.1_ASM1944400v1_genomic.fna/tc_result.tsv
[2024-01-24 14:56:04,184] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:56:04,184] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:56:04,184] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4534fb43-e00d-4134-acec-2d6b3470337a/dqc_reference/checkm_data
[2024-01-24 14:56:04,185] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:56:04,214] [INFO] Task started: CheckM
[2024-01-24 14:56:04,215] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019444005.1_ASM1944400v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019444005.1_ASM1944400v1_genomic.fna/checkm_input GCF_019444005.1_ASM1944400v1_genomic.fna/checkm_result
[2024-01-24 14:56:26,538] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:26,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:26,561] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:26,562] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:26,562] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019444005.1_ASM1944400v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:26,562] [INFO] Task started: Blastn
[2024-01-24 14:56:26,563] [INFO] Running command: blastn -query GCF_019444005.1_ASM1944400v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4534fb43-e00d-4134-acec-2d6b3470337a/dqc_reference/reference_markers_gtdb.fasta -out GCF_019444005.1_ASM1944400v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:27,325] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:27,329] [INFO] Selected 21 target genomes.
[2024-01-24 14:56:27,330] [INFO] Target genome list was writen to GCF_019444005.1_ASM1944400v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:27,345] [INFO] Task started: fastANI
[2024-01-24 14:56:27,345] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2bfb12f-50d8-4f8c-abf1-d9c9ebe3401c/GCF_019444005.1_ASM1944400v1_genomic.fna.gz --refList GCF_019444005.1_ASM1944400v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019444005.1_ASM1944400v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:35,267] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:35,279] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:35,279] [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_001434225.1	s__Liquorilactobacillus nagelii	99.9518	811	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.67	98.67	0.89	0.89	2	conclusive
GCF_000237995.1	s__Pediococcus claussenii	80.2115	50	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Pediococcus	95.0	99.87	99.79	0.97	0.95	4	-
GCF_001435235.1	s__Liquorilactobacillus ghanensis	80.149	448	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000260415.1	s__Liquorilactobacillus mali	79.2045	118	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.97	99.95	0.96	0.94	4	-
GCF_001434935.1	s__Liquorilactobacillus uvarum	79.0206	116	854	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	78.4394	192	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.24	98.67	0.86	0.83	3	-
GCF_001436755.1	s__Liquorilactobacillus aquaticus	77.8536	91	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612445.1	s__Liquorilactobacillus sucicola	77.7422	100	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001434845.1	s__Liquorilactobacillus hordei	77.5324	125	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	98.13	98.13	0.87	0.87	2	-
GCF_001436735.1	s__Liquorilactobacillus cacaonum	77.5192	115	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Liquorilactobacillus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000423245.1	s__Ligilactobacillus ceti	76.7875	56	854	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Ligilactobacillus	95.0	99.99	99.99	0.99	0.99	2	-
GCA_019114385.1	s__Ligilactobacillus excrementigallinarum	75.7728	50	854	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 14:56:35,281] [INFO] GTDB search result was written to GCF_019444005.1_ASM1944400v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:35,282] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:35,290] [INFO] DFAST_QC result json was written to GCF_019444005.1_ASM1944400v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:35,291] [INFO] DFAST_QC completed!
[2024-01-24 14:56:35,291] [INFO] Total running time: 0h0m45s