[2024-01-25 18:28:50,578] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:28:50,579] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:28:50,579] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c3b2510-b874-4169-9af3-27279ea707c5/dqc_reference
[2024-01-25 18:28:51,709] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:28:51,715] [INFO] Task started: Prodigal
[2024-01-25 18:28:51,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg178cd292-78d9-45c2-ab79-c93eaac1e7e7/GCF_012396465.1_ASM1239646v1_genomic.fna.gz | prodigal -d GCF_012396465.1_ASM1239646v1_genomic.fna/cds.fna -a GCF_012396465.1_ASM1239646v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:28:55,481] [INFO] Task succeeded: Prodigal
[2024-01-25 18:28:55,481] [INFO] Task started: HMMsearch
[2024-01-25 18:28:55,481] [INFO] Running command: hmmsearch --tblout GCF_012396465.1_ASM1239646v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c3b2510-b874-4169-9af3-27279ea707c5/dqc_reference/reference_markers.hmm GCF_012396465.1_ASM1239646v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:28:55,660] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:28:55,661] [INFO] Found 6/6 markers.
[2024-01-25 18:28:55,684] [INFO] Query marker FASTA was written to GCF_012396465.1_ASM1239646v1_genomic.fna/markers.fasta
[2024-01-25 18:28:55,684] [INFO] Task started: Blastn
[2024-01-25 18:28:55,684] [INFO] Running command: blastn -query GCF_012396465.1_ASM1239646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3b2510-b874-4169-9af3-27279ea707c5/dqc_reference/reference_markers.fasta -out GCF_012396465.1_ASM1239646v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:28:56,218] [INFO] Task succeeded: Blastn
[2024-01-25 18:28:56,222] [INFO] Selected 17 target genomes.
[2024-01-25 18:28:56,223] [INFO] Target genome list was writen to GCF_012396465.1_ASM1239646v1_genomic.fna/target_genomes.txt
[2024-01-25 18:28:56,244] [INFO] Task started: fastANI
[2024-01-25 18:28:56,244] [INFO] Running command: fastANI --query /var/lib/cwl/stg178cd292-78d9-45c2-ab79-c93eaac1e7e7/GCF_012396465.1_ASM1239646v1_genomic.fna.gz --refList GCF_012396465.1_ASM1239646v1_genomic.fna/target_genomes.txt --output GCF_012396465.1_ASM1239646v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:29:01,853] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:01,853] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c3b2510-b874-4169-9af3-27279ea707c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:29:01,854] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c3b2510-b874-4169-9af3-27279ea707c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:29:01,861] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:29:01,861] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:29:01,861] [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
Weissella soli	strain=CCUG 46608	GCA_012396465.1	155866	155866	type	True	100.0	548	549	95	conclusive
Weissella soli	strain=KACC 11848	GCA_001761545.1	155866	155866	type	True	99.9992	548	549	95	conclusive
Weissella cibaria	strain=KACC 11862	GCA_000193635.2	137591	137591	type	True	78.6011	90	549	95	below_threshold
Weissella koreensis	strain=KCTC 3621	GCA_000277645.1	165096	165096	type	True	78.5687	62	549	95	below_threshold
Weissella hellenica	strain=NBRC 15553	GCA_006540065.1	46256	46256	suspected-type	True	78.5622	61	549	95	below_threshold
Weissella cibaria	strain=JCM 12495	GCA_005405525.1	137591	137591	type	True	78.4856	89	549	95	below_threshold
Weissella uvarum	strain=B18NM42	GCA_023657405.1	1479233	1479233	type	True	78.3775	65	549	95	below_threshold
Weissella ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	78.3244	66	549	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:29:01,862] [INFO] DFAST Taxonomy check result was written to GCF_012396465.1_ASM1239646v1_genomic.fna/tc_result.tsv
[2024-01-25 18:29:01,863] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:29:01,863] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:29:01,863] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c3b2510-b874-4169-9af3-27279ea707c5/dqc_reference/checkm_data
[2024-01-25 18:29:01,864] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:29:01,883] [INFO] Task started: CheckM
[2024-01-25 18:29:01,883] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396465.1_ASM1239646v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396465.1_ASM1239646v1_genomic.fna/checkm_input GCF_012396465.1_ASM1239646v1_genomic.fna/checkm_result
[2024-01-25 18:29:19,161] [INFO] Task succeeded: CheckM
[2024-01-25 18:29:19,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:29:19,185] [INFO] ===== Completeness check finished =====
[2024-01-25 18:29:19,185] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:29:19,185] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396465.1_ASM1239646v1_genomic.fna/markers.fasta)
[2024-01-25 18:29:19,186] [INFO] Task started: Blastn
[2024-01-25 18:29:19,186] [INFO] Running command: blastn -query GCF_012396465.1_ASM1239646v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c3b2510-b874-4169-9af3-27279ea707c5/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396465.1_ASM1239646v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:29:19,906] [INFO] Task succeeded: Blastn
[2024-01-25 18:29:19,910] [INFO] Selected 22 target genomes.
[2024-01-25 18:29:19,910] [INFO] Target genome list was writen to GCF_012396465.1_ASM1239646v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:29:19,957] [INFO] Task started: fastANI
[2024-01-25 18:29:19,957] [INFO] Running command: fastANI --query /var/lib/cwl/stg178cd292-78d9-45c2-ab79-c93eaac1e7e7/GCF_012396465.1_ASM1239646v1_genomic.fna.gz --refList GCF_012396465.1_ASM1239646v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396465.1_ASM1239646v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:29:27,021] [INFO] Task succeeded: fastANI
[2024-01-25 18:29:27,028] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:29:27,028] [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_001761545.1	s__Weissella soli	99.9992	548	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.70	98.78	0.98	0.93	5	conclusive
GCF_004521965.1	s__Weissella cibaria_A	78.905	91	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001436895.1	s__Weissella confusa	78.8264	105	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_004771295.1	s__Weissella confusa_B	78.8078	109	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.67	96.65	0.95	0.87	5	-
GCF_000277645.1	s__Weissella koreensis	78.6824	61	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.29	98.85	0.93	0.91	5	-
GCF_004766315.1	s__Weissella confusa_A	78.6191	105	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000193635.1	s__Weissella cibaria	78.6074	91	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.01	95.59	0.95	0.88	53	-
GCF_005405465.1	s__Weissella thailandensis	78.4032	67	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.06	96.27	0.98	0.95	5	-
GCF_018394055.1	s__Weissella ceti	78.381	65	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016908785.1	s__Weissella uvarum	78.335	63	549	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:29:27,030] [INFO] GTDB search result was written to GCF_012396465.1_ASM1239646v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:29:27,031] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:29:27,033] [INFO] DFAST_QC result json was written to GCF_012396465.1_ASM1239646v1_genomic.fna/dqc_result.json
[2024-01-25 18:29:27,033] [INFO] DFAST_QC completed!
[2024-01-25 18:29:27,033] [INFO] Total running time: 0h0m36s