[2024-01-24 15:27:20,824] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:27:20,826] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:27:20,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg55c9b168-87ea-40a0-8b31-102b5e497082/dqc_reference
[2024-01-24 15:27:23,289] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:27:23,290] [INFO] Task started: Prodigal
[2024-01-24 15:27:23,290] [INFO] Running command: gunzip -c /var/lib/cwl/stg21bc9999-2a99-40ab-929c-4e58efa4eb5d/GCF_009659375.1_ASM965937v1_genomic.fna.gz | prodigal -d GCF_009659375.1_ASM965937v1_genomic.fna/cds.fna -a GCF_009659375.1_ASM965937v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:28,976] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:28,976] [INFO] Task started: HMMsearch
[2024-01-24 15:27:28,976] [INFO] Running command: hmmsearch --tblout GCF_009659375.1_ASM965937v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55c9b168-87ea-40a0-8b31-102b5e497082/dqc_reference/reference_markers.hmm GCF_009659375.1_ASM965937v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:29,230] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:29,232] [INFO] Found 6/6 markers.
[2024-01-24 15:27:29,260] [INFO] Query marker FASTA was written to GCF_009659375.1_ASM965937v1_genomic.fna/markers.fasta
[2024-01-24 15:27:29,261] [INFO] Task started: Blastn
[2024-01-24 15:27:29,261] [INFO] Running command: blastn -query GCF_009659375.1_ASM965937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55c9b168-87ea-40a0-8b31-102b5e497082/dqc_reference/reference_markers.fasta -out GCF_009659375.1_ASM965937v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:30,366] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:30,381] [INFO] Selected 26 target genomes.
[2024-01-24 15:27:30,382] [INFO] Target genome list was writen to GCF_009659375.1_ASM965937v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:30,489] [INFO] Task started: fastANI
[2024-01-24 15:27:30,490] [INFO] Running command: fastANI --query /var/lib/cwl/stg21bc9999-2a99-40ab-929c-4e58efa4eb5d/GCF_009659375.1_ASM965937v1_genomic.fna.gz --refList GCF_009659375.1_ASM965937v1_genomic.fna/target_genomes.txt --output GCF_009659375.1_ASM965937v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:42,839] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:42,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55c9b168-87ea-40a0-8b31-102b5e497082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:42,841] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55c9b168-87ea-40a0-8b31-102b5e497082/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:42,854] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:42,854] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:42,854] [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
Fundicoccus ignavus	strain=DSM 109652	GCA_009659375.1	2664442	2664442	type	True	100.0	969	974	95	conclusive
Globicatella sulfidifaciens	strain=DSM 15739	GCA_900167405.1	136093	136093	type	True	78.868	92	974	95	below_threshold
Vaginisenegalia massiliensis	strain=Marseille-P5643	GCA_900604935.1	2058294	2058294	type	True	78.4033	50	974	95	below_threshold
Globicatella sanguinis	strain=NBRC 15551	GCA_001552295.1	13076	13076	type	True	78.2386	79	974	95	below_threshold
Ruoffia halotolerans	strain=INB8	GCA_014049385.1	2748684	2748684	type	True	77.87	100	974	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:42,856] [INFO] DFAST Taxonomy check result was written to GCF_009659375.1_ASM965937v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:42,861] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:42,861] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:42,862] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55c9b168-87ea-40a0-8b31-102b5e497082/dqc_reference/checkm_data
[2024-01-24 15:27:42,863] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:42,901] [INFO] Task started: CheckM
[2024-01-24 15:27:42,902] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009659375.1_ASM965937v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009659375.1_ASM965937v1_genomic.fna/checkm_input GCF_009659375.1_ASM965937v1_genomic.fna/checkm_result
[2024-01-24 15:28:08,706] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:08,707] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:08,729] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:08,729] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:08,729] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009659375.1_ASM965937v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:08,730] [INFO] Task started: Blastn
[2024-01-24 15:28:08,730] [INFO] Running command: blastn -query GCF_009659375.1_ASM965937v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55c9b168-87ea-40a0-8b31-102b5e497082/dqc_reference/reference_markers_gtdb.fasta -out GCF_009659375.1_ASM965937v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:09,527] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:09,531] [INFO] Selected 23 target genomes.
[2024-01-24 15:28:09,531] [INFO] Target genome list was writen to GCF_009659375.1_ASM965937v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:09,554] [INFO] Task started: fastANI
[2024-01-24 15:28:09,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg21bc9999-2a99-40ab-929c-4e58efa4eb5d/GCF_009659375.1_ASM965937v1_genomic.fna.gz --refList GCF_009659375.1_ASM965937v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009659375.1_ASM965937v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:19,565] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:19,573] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:28:19,574] [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_009659375.1	s__Fundicoccus ignavus	100.0	969	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Fundicoccus	95.0	98.16	98.10	0.87	0.87	3	conclusive
GCA_015863215.1	s__DSM-111022 sp015863215	79.7753	77	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__DSM-111022	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015863195.1	s__DSM-111022 sp015863195	79.0359	81	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__DSM-111022	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900167405.1	s__Globicatella sulfidifaciens	78.868	92	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	97.81	97.81	0.71	0.71	2	-
GCF_005864045.1	s__Facklamia_A tabacinasalis	78.5578	114	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia_A	95.0	96.44	96.27	0.84	0.80	4	-
GCF_001552295.1	s__Globicatella sanguinis	78.2386	79	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	97.13	96.22	0.85	0.84	3	-
GCA_016237705.1	s__Globicatella sp010892315	77.9574	83	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Globicatella	95.0	98.61	97.07	0.93	0.84	6	-
GCA_014049385.1	s__Facklamia_A sp014049385	77.8662	100	974	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Facklamia_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:28:19,575] [INFO] GTDB search result was written to GCF_009659375.1_ASM965937v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:19,576] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:19,579] [INFO] DFAST_QC result json was written to GCF_009659375.1_ASM965937v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:19,579] [INFO] DFAST_QC completed!
[2024-01-24 15:28:19,579] [INFO] Total running time: 0h0m59s