[2024-01-24 14:07:00,075] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:07:00,077] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:07:00,077] [INFO] DQC Reference Directory: /var/lib/cwl/stg9f71f01c-9b92-4401-8b62-73a507c78986/dqc_reference
[2024-01-24 14:07:01,448] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:01,449] [INFO] Task started: Prodigal
[2024-01-24 14:07:01,449] [INFO] Running command: gunzip -c /var/lib/cwl/stg4d6cc913-d7be-445b-9354-0e24694a92b5/GCF_900460455.1_54984_H01_genomic.fna.gz | prodigal -d GCF_900460455.1_54984_H01_genomic.fna/cds.fna -a GCF_900460455.1_54984_H01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:05,274] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:05,275] [INFO] Task started: HMMsearch
[2024-01-24 14:07:05,275] [INFO] Running command: hmmsearch --tblout GCF_900460455.1_54984_H01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9f71f01c-9b92-4401-8b62-73a507c78986/dqc_reference/reference_markers.hmm GCF_900460455.1_54984_H01_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:05,418] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:05,420] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4d6cc913-d7be-445b-9354-0e24694a92b5/GCF_900460455.1_54984_H01_genomic.fna.gz]
[2024-01-24 14:07:05,441] [INFO] Query marker FASTA was written to GCF_900460455.1_54984_H01_genomic.fna/markers.fasta
[2024-01-24 14:07:05,441] [INFO] Task started: Blastn
[2024-01-24 14:07:05,441] [INFO] Running command: blastn -query GCF_900460455.1_54984_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f71f01c-9b92-4401-8b62-73a507c78986/dqc_reference/reference_markers.fasta -out GCF_900460455.1_54984_H01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:05,978] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:05,982] [INFO] Selected 11 target genomes.
[2024-01-24 14:07:05,982] [INFO] Target genome list was writen to GCF_900460455.1_54984_H01_genomic.fna/target_genomes.txt
[2024-01-24 14:07:05,997] [INFO] Task started: fastANI
[2024-01-24 14:07:05,997] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d6cc913-d7be-445b-9354-0e24694a92b5/GCF_900460455.1_54984_H01_genomic.fna.gz --refList GCF_900460455.1_54984_H01_genomic.fna/target_genomes.txt --output GCF_900460455.1_54984_H01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:10,440] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:10,440] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9f71f01c-9b92-4401-8b62-73a507c78986/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:10,441] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9f71f01c-9b92-4401-8b62-73a507c78986/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:10,448] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:07:10,448] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:10,448] [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 viridescens	strain=NCTC13645	GCA_900460455.1	1629	1629	type	True	100.0	513	513	95	conclusive
Weissella viridescens	strain=DSM 20410	GCA_001437355.1	1629	1629	type	True	99.6764	499	513	95	conclusive
Weissella viridescens	strain=NCDO 1655	GCA_001460875.1	1629	1629	type	True	99.0047	386	513	95	conclusive
Weissella ceti	strain=CECT 7719	GCA_018394055.1	759620	759620	suspected-type	True	80.6938	99	513	95	below_threshold
Weissella minor	strain=DSM 20014	GCA_001437425.1	1620	1620	type	True	80.0231	239	513	95	below_threshold
Weissella uvarum	strain=DSM 28060	GCA_016908785.1	1479233	1479233	type	True	79.9589	198	513	95	below_threshold
Weissella uvarum	strain=B18NM42	GCA_023657405.1	1479233	1479233	type	True	79.9063	197	513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:10,449] [INFO] DFAST Taxonomy check result was written to GCF_900460455.1_54984_H01_genomic.fna/tc_result.tsv
[2024-01-24 14:07:10,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:10,450] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:10,450] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9f71f01c-9b92-4401-8b62-73a507c78986/dqc_reference/checkm_data
[2024-01-24 14:07:10,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:10,471] [INFO] Task started: CheckM
[2024-01-24 14:07:10,471] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460455.1_54984_H01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460455.1_54984_H01_genomic.fna/checkm_input GCF_900460455.1_54984_H01_genomic.fna/checkm_result
[2024-01-24 14:07:28,548] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:28,549] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.52%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:28,565] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:28,566] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:28,566] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460455.1_54984_H01_genomic.fna/markers.fasta)
[2024-01-24 14:07:28,566] [INFO] Task started: Blastn
[2024-01-24 14:07:28,566] [INFO] Running command: blastn -query GCF_900460455.1_54984_H01_genomic.fna/markers.fasta -db /var/lib/cwl/stg9f71f01c-9b92-4401-8b62-73a507c78986/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460455.1_54984_H01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:29,261] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:29,265] [INFO] Selected 12 target genomes.
[2024-01-24 14:07:29,265] [INFO] Target genome list was writen to GCF_900460455.1_54984_H01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:29,278] [INFO] Task started: fastANI
[2024-01-24 14:07:29,279] [INFO] Running command: fastANI --query /var/lib/cwl/stg4d6cc913-d7be-445b-9354-0e24694a92b5/GCF_900460455.1_54984_H01_genomic.fna.gz --refList GCF_900460455.1_54984_H01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460455.1_54984_H01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:33,317] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:33,327] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:33,327] [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_001437355.1	s__Weissella viridescens	99.6764	499	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.44	98.29	0.96	0.91	6	conclusive
GCF_003862435.1	s__Weissella viridescens_A	85.697	425	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018394055.1	s__Weissella ceti	80.7999	98	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001437425.1	s__Weissella minor	80.0231	239	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	95.93	95.93	0.88	0.88	2	-
GCF_016908785.1	s__Weissella uvarum	79.9871	197	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004771295.1	s__Weissella confusa_B	79.68	108	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.67	96.65	0.95	0.87	5	-
GCF_004766315.1	s__Weissella confusa_A	78.9967	100	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004521965.1	s__Weissella cibaria_A	78.9762	83	513	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	78.9557	106	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	98.10	97.29	0.91	0.88	80	-
GCF_000420365.1	s__Weissella halotolerans	78.8199	64	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000691805.2	s__Weissella oryzae	78.6149	72	513	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Lactobacillaceae;g__Weissella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:33,329] [INFO] GTDB search result was written to GCF_900460455.1_54984_H01_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:33,329] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:33,333] [INFO] DFAST_QC result json was written to GCF_900460455.1_54984_H01_genomic.fna/dqc_result.json
[2024-01-24 14:07:33,333] [INFO] DFAST_QC completed!
[2024-01-24 14:07:33,333] [INFO] Total running time: 0h0m33s