[2024-01-24 11:26:12,726] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:26:12,729] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:26:12,729] [INFO] DQC Reference Directory: /var/lib/cwl/stg7c346f79-6047-4943-8515-958e672e3f8a/dqc_reference
[2024-01-24 11:26:14,105] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:26:14,106] [INFO] Task started: Prodigal
[2024-01-24 11:26:14,106] [INFO] Running command: gunzip -c /var/lib/cwl/stg86d6cd28-fca7-446d-9578-932191a1ae95/GCF_025150565.1_ASM2515056v1_genomic.fna.gz | prodigal -d GCF_025150565.1_ASM2515056v1_genomic.fna/cds.fna -a GCF_025150565.1_ASM2515056v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:26:18,297] [INFO] Task succeeded: Prodigal
[2024-01-24 11:26:18,297] [INFO] Task started: HMMsearch
[2024-01-24 11:26:18,297] [INFO] Running command: hmmsearch --tblout GCF_025150565.1_ASM2515056v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7c346f79-6047-4943-8515-958e672e3f8a/dqc_reference/reference_markers.hmm GCF_025150565.1_ASM2515056v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:26:18,589] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:26:18,590] [INFO] Found 6/6 markers.
[2024-01-24 11:26:18,619] [INFO] Query marker FASTA was written to GCF_025150565.1_ASM2515056v1_genomic.fna/markers.fasta
[2024-01-24 11:26:18,619] [INFO] Task started: Blastn
[2024-01-24 11:26:18,619] [INFO] Running command: blastn -query GCF_025150565.1_ASM2515056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c346f79-6047-4943-8515-958e672e3f8a/dqc_reference/reference_markers.fasta -out GCF_025150565.1_ASM2515056v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:19,312] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:19,315] [INFO] Selected 17 target genomes.
[2024-01-24 11:26:19,316] [INFO] Target genome list was writen to GCF_025150565.1_ASM2515056v1_genomic.fna/target_genomes.txt
[2024-01-24 11:26:19,340] [INFO] Task started: fastANI
[2024-01-24 11:26:19,340] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d6cd28-fca7-446d-9578-932191a1ae95/GCF_025150565.1_ASM2515056v1_genomic.fna.gz --refList GCF_025150565.1_ASM2515056v1_genomic.fna/target_genomes.txt --output GCF_025150565.1_ASM2515056v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:26:26,316] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:26,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7c346f79-6047-4943-8515-958e672e3f8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:26:26,317] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7c346f79-6047-4943-8515-958e672e3f8a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:26:26,322] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 11:26:26,323] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:26:26,323] [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
Granulicatella adiacens	strain=ATCC 49175	GCA_025150565.1	46124	46124	type	True	100.0	653	655	95	conclusive
Granulicatella adiacens	strain=FDAARGOS_1477	GCA_019931005.1	46124	46124	type	True	99.9989	652	655	95	conclusive
Granulicatella adiacens	strain=ATCC 49175	GCA_000160675.1	46124	46124	type	True	99.9356	641	655	95	conclusive
Carnobacterium gallinarum	strain=MT44	GCA_000744375.1	2749	2749	type	True	79.4152	50	655	95	below_threshold
Granulicatella balaenopterae	strain=DSM 15827	GCA_900111135.1	137733	137733	type	True	78.9691	90	655	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:26:26,325] [INFO] DFAST Taxonomy check result was written to GCF_025150565.1_ASM2515056v1_genomic.fna/tc_result.tsv
[2024-01-24 11:26:26,325] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:26:26,325] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:26:26,326] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7c346f79-6047-4943-8515-958e672e3f8a/dqc_reference/checkm_data
[2024-01-24 11:26:26,327] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:26:26,349] [INFO] Task started: CheckM
[2024-01-24 11:26:26,349] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025150565.1_ASM2515056v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025150565.1_ASM2515056v1_genomic.fna/checkm_input GCF_025150565.1_ASM2515056v1_genomic.fna/checkm_result
[2024-01-24 11:26:47,325] [INFO] Task succeeded: CheckM
[2024-01-24 11:26:47,326] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:26:47,345] [INFO] ===== Completeness check finished =====
[2024-01-24 11:26:47,345] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:26:47,345] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025150565.1_ASM2515056v1_genomic.fna/markers.fasta)
[2024-01-24 11:26:47,346] [INFO] Task started: Blastn
[2024-01-24 11:26:47,346] [INFO] Running command: blastn -query GCF_025150565.1_ASM2515056v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7c346f79-6047-4943-8515-958e672e3f8a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025150565.1_ASM2515056v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:26:48,177] [INFO] Task succeeded: Blastn
[2024-01-24 11:26:48,180] [INFO] Selected 9 target genomes.
[2024-01-24 11:26:48,180] [INFO] Target genome list was writen to GCF_025150565.1_ASM2515056v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:26:48,191] [INFO] Task started: fastANI
[2024-01-24 11:26:48,191] [INFO] Running command: fastANI --query /var/lib/cwl/stg86d6cd28-fca7-446d-9578-932191a1ae95/GCF_025150565.1_ASM2515056v1_genomic.fna.gz --refList GCF_025150565.1_ASM2515056v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025150565.1_ASM2515056v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:26:51,944] [INFO] Task succeeded: fastANI
[2024-01-24 11:26:51,952] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:26:51,952] [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_000160675.1	s__Granulicatella adiacens	99.9356	641	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	96.49	96.38	0.91	0.88	11	conclusive
GCA_905371865.1	s__Granulicatella sp905371865	92.825	324	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900551535.1	s__Granulicatella sp900551535	88.4719	330	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001071995.1	s__Granulicatella sp001071995	88.3845	454	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001058355.1	s__Granulicatella sp001058355	88.0728	324	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	95.40	95.27	0.77	0.71	6	-
GCA_018364485.1	s__Granulicatella adiacens_A	87.8202	419	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015264885.1	s__Granulicatella sp015264885	87.6299	287	655	d__Bacteria;p__Firmicutes;c__Bacilli;o__Lactobacillales;f__Aerococcaceae;g__Granulicatella	95.0	95.15	95.15	0.88	0.88	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:26:51,954] [INFO] GTDB search result was written to GCF_025150565.1_ASM2515056v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:26:51,955] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:26:51,959] [INFO] DFAST_QC result json was written to GCF_025150565.1_ASM2515056v1_genomic.fna/dqc_result.json
[2024-01-24 11:26:51,959] [INFO] DFAST_QC completed!
[2024-01-24 11:26:51,959] [INFO] Total running time: 0h0m39s