[2023-06-30 19:32:56,865] [INFO] DFAST_QC pipeline started.
[2023-06-30 19:32:56,869] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 19:32:56,869] [INFO] DQC Reference Directory: /var/lib/cwl/stg25c263ef-d6d3-433b-a646-c4d6c265aaf8/dqc_reference
[2023-06-30 19:32:58,437] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 19:32:58,438] [INFO] Task started: Prodigal
[2023-06-30 19:32:58,438] [INFO] Running command: gunzip -c /var/lib/cwl/stg1673313b-388c-4dfd-954e-9bc05877b1f4/GCA_024711265.1_ASM2471126v1_genomic.fna.gz | prodigal -d GCA_024711265.1_ASM2471126v1_genomic.fna/cds.fna -a GCA_024711265.1_ASM2471126v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 19:33:06,215] [INFO] Task succeeded: Prodigal
[2023-06-30 19:33:06,215] [INFO] Task started: HMMsearch
[2023-06-30 19:33:06,215] [INFO] Running command: hmmsearch --tblout GCA_024711265.1_ASM2471126v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg25c263ef-d6d3-433b-a646-c4d6c265aaf8/dqc_reference/reference_markers.hmm GCA_024711265.1_ASM2471126v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 19:33:06,494] [INFO] Task succeeded: HMMsearch
[2023-06-30 19:33:06,495] [INFO] Found 6/6 markers.
[2023-06-30 19:33:06,530] [INFO] Query marker FASTA was written to GCA_024711265.1_ASM2471126v1_genomic.fna/markers.fasta
[2023-06-30 19:33:06,530] [INFO] Task started: Blastn
[2023-06-30 19:33:06,530] [INFO] Running command: blastn -query GCA_024711265.1_ASM2471126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c263ef-d6d3-433b-a646-c4d6c265aaf8/dqc_reference/reference_markers.fasta -out GCA_024711265.1_ASM2471126v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:33:07,167] [INFO] Task succeeded: Blastn
[2023-06-30 19:33:07,171] [INFO] Selected 17 target genomes.
[2023-06-30 19:33:07,171] [INFO] Target genome list was writen to GCA_024711265.1_ASM2471126v1_genomic.fna/target_genomes.txt
[2023-06-30 19:33:07,197] [INFO] Task started: fastANI
[2023-06-30 19:33:07,197] [INFO] Running command: fastANI --query /var/lib/cwl/stg1673313b-388c-4dfd-954e-9bc05877b1f4/GCA_024711265.1_ASM2471126v1_genomic.fna.gz --refList GCA_024711265.1_ASM2471126v1_genomic.fna/target_genomes.txt --output GCA_024711265.1_ASM2471126v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 19:33:16,151] [INFO] Task succeeded: fastANI
[2023-06-30 19:33:16,152] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg25c263ef-d6d3-433b-a646-c4d6c265aaf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 19:33:16,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg25c263ef-d6d3-433b-a646-c4d6c265aaf8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 19:33:16,157] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 19:33:16,157] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 19:33:16,157] [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
Bdellovibrio bacteriovorus	strain=HD100	GCA_000196175.1	959	959	suspected-type	True	78.8045	303	846	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 19:33:16,160] [INFO] DFAST Taxonomy check result was written to GCA_024711265.1_ASM2471126v1_genomic.fna/tc_result.tsv
[2023-06-30 19:33:16,160] [INFO] ===== Taxonomy check completed =====
[2023-06-30 19:33:16,161] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 19:33:16,161] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg25c263ef-d6d3-433b-a646-c4d6c265aaf8/dqc_reference/checkm_data
[2023-06-30 19:33:16,162] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 19:33:16,202] [INFO] Task started: CheckM
[2023-06-30 19:33:16,203] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024711265.1_ASM2471126v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024711265.1_ASM2471126v1_genomic.fna/checkm_input GCA_024711265.1_ASM2471126v1_genomic.fna/checkm_result
[2023-06-30 19:33:45,787] [INFO] Task succeeded: CheckM
[2023-06-30 19:33:45,789] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 19:33:45,810] [INFO] ===== Completeness check finished =====
[2023-06-30 19:33:45,811] [INFO] ===== Start GTDB Search =====
[2023-06-30 19:33:45,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024711265.1_ASM2471126v1_genomic.fna/markers.fasta)
[2023-06-30 19:33:45,812] [INFO] Task started: Blastn
[2023-06-30 19:33:45,812] [INFO] Running command: blastn -query GCA_024711265.1_ASM2471126v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg25c263ef-d6d3-433b-a646-c4d6c265aaf8/dqc_reference/reference_markers_gtdb.fasta -out GCA_024711265.1_ASM2471126v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 19:33:46,830] [INFO] Task succeeded: Blastn
[2023-06-30 19:33:46,834] [INFO] Selected 14 target genomes.
[2023-06-30 19:33:46,834] [INFO] Target genome list was writen to GCA_024711265.1_ASM2471126v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 19:33:46,866] [INFO] Task started: fastANI
[2023-06-30 19:33:46,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg1673313b-388c-4dfd-954e-9bc05877b1f4/GCA_024711265.1_ASM2471126v1_genomic.fna.gz --refList GCA_024711265.1_ASM2471126v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024711265.1_ASM2471126v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 19:33:55,054] [INFO] Task succeeded: fastANI
[2023-06-30 19:33:55,065] [INFO] Found 12 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 19:33:55,065] [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
GCA_019104905.1	s__Bdellovibrio sp019104905	88.0881	593	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592745.1	s__Bdellovibrio bacteriovorus_B	79.7892	346	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001592755.1	s__Bdellovibrio bacteriovorus_E	79.5046	364	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000786105.1	s__Bdellovibrio sp000786105	79.331	329	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000317895.1	s__Bdellovibrio bacteriovorus_F	78.9303	305	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000196175.1	s__Bdellovibrio bacteriovorus	78.7959	303	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	98.95	98.95	0.97	0.97	2	-
GCF_002208115.1	s__Bdellovibrio bacteriovorus_C	78.6813	300	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874625.1	s__Bdellovibrio sp006874625	78.5921	213	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013360185.1	s__Bdellovibrio sp013360185	78.5845	257	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002209355.1	s__Bdellovibrio sp002209355	78.5747	171	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006874645.1	s__Bdellovibrio sp006874645	78.3113	194	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002381805.1	s__Bdellovibrio sp002381805	78.0993	172	846	d__Bacteria;p__Bdellovibrionota;c__Bdellovibrionia;o__Bdellovibrionales;f__Bdellovibrionaceae;g__Bdellovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 19:33:55,068] [INFO] GTDB search result was written to GCA_024711265.1_ASM2471126v1_genomic.fna/result_gtdb.tsv
[2023-06-30 19:33:55,068] [INFO] ===== GTDB Search completed =====
[2023-06-30 19:33:55,071] [INFO] DFAST_QC result json was written to GCA_024711265.1_ASM2471126v1_genomic.fna/dqc_result.json
[2023-06-30 19:33:55,071] [INFO] DFAST_QC completed!
[2023-06-30 19:33:55,071] [INFO] Total running time: 0h0m58s