[2023-06-29 12:54:49,781] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:54:49,784] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:54:49,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg9cfe4daa-0ff3-4040-b7f2-e205f8047049/dqc_reference
[2023-06-29 12:54:50,975] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:54:50,976] [INFO] Task started: Prodigal
[2023-06-29 12:54:50,976] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ee5a81c-0f5d-48a9-b41e-f4f5939af3a0/GCA_023954635.1_ASM2395463v1_genomic.fna.gz | prodigal -d GCA_023954635.1_ASM2395463v1_genomic.fna/cds.fna -a GCA_023954635.1_ASM2395463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:54:57,335] [INFO] Task succeeded: Prodigal
[2023-06-29 12:54:57,335] [INFO] Task started: HMMsearch
[2023-06-29 12:54:57,335] [INFO] Running command: hmmsearch --tblout GCA_023954635.1_ASM2395463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9cfe4daa-0ff3-4040-b7f2-e205f8047049/dqc_reference/reference_markers.hmm GCA_023954635.1_ASM2395463v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:54:57,650] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:54:57,655] [INFO] Found 6/6 markers.
[2023-06-29 12:54:57,709] [INFO] Query marker FASTA was written to GCA_023954635.1_ASM2395463v1_genomic.fna/markers.fasta
[2023-06-29 12:54:57,709] [INFO] Task started: Blastn
[2023-06-29 12:54:57,710] [INFO] Running command: blastn -query GCA_023954635.1_ASM2395463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cfe4daa-0ff3-4040-b7f2-e205f8047049/dqc_reference/reference_markers.fasta -out GCA_023954635.1_ASM2395463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:54:58,324] [INFO] Task succeeded: Blastn
[2023-06-29 12:54:58,329] [INFO] Selected 28 target genomes.
[2023-06-29 12:54:58,330] [INFO] Target genome list was writen to GCA_023954635.1_ASM2395463v1_genomic.fna/target_genomes.txt
[2023-06-29 12:54:58,344] [INFO] Task started: fastANI
[2023-06-29 12:54:58,344] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee5a81c-0f5d-48a9-b41e-f4f5939af3a0/GCA_023954635.1_ASM2395463v1_genomic.fna.gz --refList GCA_023954635.1_ASM2395463v1_genomic.fna/target_genomes.txt --output GCA_023954635.1_ASM2395463v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:55:12,686] [INFO] Task succeeded: fastANI
[2023-06-29 12:55:12,687] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9cfe4daa-0ff3-4040-b7f2-e205f8047049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:55:12,687] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9cfe4daa-0ff3-4040-b7f2-e205f8047049/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:55:12,694] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 12:55:12,694] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 12:55:12,694] [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
Halobacteriovorax marinus	strain=SJ	GCA_000210915.2	97084	97084	type	True	76.2746	61	1128	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:55:12,697] [INFO] DFAST Taxonomy check result was written to GCA_023954635.1_ASM2395463v1_genomic.fna/tc_result.tsv
[2023-06-29 12:55:12,697] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:55:12,697] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:55:12,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9cfe4daa-0ff3-4040-b7f2-e205f8047049/dqc_reference/checkm_data
[2023-06-29 12:55:12,699] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:55:12,741] [INFO] Task started: CheckM
[2023-06-29 12:55:12,741] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023954635.1_ASM2395463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023954635.1_ASM2395463v1_genomic.fna/checkm_input GCA_023954635.1_ASM2395463v1_genomic.fna/checkm_result
[2023-06-29 12:55:39,157] [INFO] Task succeeded: CheckM
[2023-06-29 12:55:39,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-29 12:55:39,186] [INFO] ===== Completeness check finished =====
[2023-06-29 12:55:39,186] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:55:39,187] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023954635.1_ASM2395463v1_genomic.fna/markers.fasta)
[2023-06-29 12:55:39,187] [INFO] Task started: Blastn
[2023-06-29 12:55:39,187] [INFO] Running command: blastn -query GCA_023954635.1_ASM2395463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9cfe4daa-0ff3-4040-b7f2-e205f8047049/dqc_reference/reference_markers_gtdb.fasta -out GCA_023954635.1_ASM2395463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:55:40,009] [INFO] Task succeeded: Blastn
[2023-06-29 12:55:40,014] [INFO] Selected 27 target genomes.
[2023-06-29 12:55:40,014] [INFO] Target genome list was writen to GCA_023954635.1_ASM2395463v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:55:40,062] [INFO] Task started: fastANI
[2023-06-29 12:55:40,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ee5a81c-0f5d-48a9-b41e-f4f5939af3a0/GCA_023954635.1_ASM2395463v1_genomic.fna.gz --refList GCA_023954635.1_ASM2395463v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023954635.1_ASM2395463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:55:54,126] [INFO] Task succeeded: fastANI
[2023-06-29 12:55:54,140] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 12:55:54,141] [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_002720865.1	s__GCA-2720865 sp002720865	79.3453	73	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__GCA-2720865	95.0	N/A	N/A	N/A	N/A	1	-
GCA_006226755.1	s__M0603 sp006226755	77.51	278	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__M0603	95.0	99.03	99.03	0.90	0.90	2	-
GCA_002753895.1	s__Halobacteriovorax sp002753895	76.7084	67	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002366565.1	s__Halobacteriovorax sp002366565	76.6543	66	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000210915.2	s__Halobacteriovorax marinus	76.3048	60	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	98.02	98.02	0.94	0.94	2	-
GCA_002163155.1	s__Halobacteriovorax marinus_A	76.3011	61	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__Halobacteriovorax	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001874305.1	s__DB6-IX sp001874305	76.1026	55	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018675575.1	s__M0603 sp018675575	76.006	76	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__M0603	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447795.1	s__DB6-IX sp000447795	75.98	54	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__DB6-IX	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000447755.1	s__BSW11-IV sp000447755	75.9692	56	1128	d__Bacteria;p__Bdellovibrionota;c__Bacteriovoracia;o__Bacteriovoracales;f__Bacteriovoracaceae;g__BSW11-IV	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 12:55:54,143] [INFO] GTDB search result was written to GCA_023954635.1_ASM2395463v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:55:54,143] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:55:54,146] [INFO] DFAST_QC result json was written to GCA_023954635.1_ASM2395463v1_genomic.fna/dqc_result.json
[2023-06-29 12:55:54,147] [INFO] DFAST_QC completed!
[2023-06-29 12:55:54,147] [INFO] Total running time: 0h1m4s