[2023-06-17 07:31:25,749] [INFO] DFAST_QC pipeline started.
[2023-06-17 07:31:25,751] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 07:31:25,751] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd7ee1ab-0632-469c-b61f-b63bbaf41902/dqc_reference
[2023-06-17 07:31:27,423] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 07:31:27,424] [INFO] Task started: Prodigal
[2023-06-17 07:31:27,424] [INFO] Running command: gunzip -c /var/lib/cwl/stg826d1ea7-d4ed-4fb4-906c-4b64dbe072d8/GCA_028708195.1_ASM2870819v1_genomic.fna.gz | prodigal -d GCA_028708195.1_ASM2870819v1_genomic.fna/cds.fna -a GCA_028708195.1_ASM2870819v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 07:31:33,828] [INFO] Task succeeded: Prodigal
[2023-06-17 07:31:33,829] [INFO] Task started: HMMsearch
[2023-06-17 07:31:33,830] [INFO] Running command: hmmsearch --tblout GCA_028708195.1_ASM2870819v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd7ee1ab-0632-469c-b61f-b63bbaf41902/dqc_reference/reference_markers.hmm GCA_028708195.1_ASM2870819v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 07:31:34,064] [INFO] Task succeeded: HMMsearch
[2023-06-17 07:31:34,066] [INFO] Found 6/6 markers.
[2023-06-17 07:31:34,093] [INFO] Query marker FASTA was written to GCA_028708195.1_ASM2870819v1_genomic.fna/markers.fasta
[2023-06-17 07:31:34,093] [INFO] Task started: Blastn
[2023-06-17 07:31:34,093] [INFO] Running command: blastn -query GCA_028708195.1_ASM2870819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7ee1ab-0632-469c-b61f-b63bbaf41902/dqc_reference/reference_markers.fasta -out GCA_028708195.1_ASM2870819v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:31:34,735] [INFO] Task succeeded: Blastn
[2023-06-17 07:31:34,740] [INFO] Selected 14 target genomes.
[2023-06-17 07:31:34,741] [INFO] Target genome list was writen to GCA_028708195.1_ASM2870819v1_genomic.fna/target_genomes.txt
[2023-06-17 07:31:34,742] [INFO] Task started: fastANI
[2023-06-17 07:31:34,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg826d1ea7-d4ed-4fb4-906c-4b64dbe072d8/GCA_028708195.1_ASM2870819v1_genomic.fna.gz --refList GCA_028708195.1_ASM2870819v1_genomic.fna/target_genomes.txt --output GCA_028708195.1_ASM2870819v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 07:31:44,339] [INFO] Task succeeded: fastANI
[2023-06-17 07:31:44,340] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd7ee1ab-0632-469c-b61f-b63bbaf41902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 07:31:44,341] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd7ee1ab-0632-469c-b61f-b63bbaf41902/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 07:31:44,353] [INFO] Found 7 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 07:31:44,353] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 07:31:44,353] [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
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	86.561	524	598	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	78.5079	245	598	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	78.2196	236	598	95	below_threshold
Desulfovibrio piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	77.922	158	598	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	76.9662	87	598	95	below_threshold
Cupidesulfovibrio oxamicus	strain=NCIMB 9442	GCA_015731765.1	32016	32016	type	True	76.8385	80	598	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	76.1984	52	598	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 07:31:44,356] [INFO] DFAST Taxonomy check result was written to GCA_028708195.1_ASM2870819v1_genomic.fna/tc_result.tsv
[2023-06-17 07:31:44,356] [INFO] ===== Taxonomy check completed =====
[2023-06-17 07:31:44,356] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 07:31:44,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd7ee1ab-0632-469c-b61f-b63bbaf41902/dqc_reference/checkm_data
[2023-06-17 07:31:44,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 07:31:44,388] [INFO] Task started: CheckM
[2023-06-17 07:31:44,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708195.1_ASM2870819v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708195.1_ASM2870819v1_genomic.fna/checkm_input GCA_028708195.1_ASM2870819v1_genomic.fna/checkm_result
[2023-06-17 07:32:09,262] [INFO] Task succeeded: CheckM
[2023-06-17 07:32:09,263] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.51%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 07:32:09,285] [INFO] ===== Completeness check finished =====
[2023-06-17 07:32:09,286] [INFO] ===== Start GTDB Search =====
[2023-06-17 07:32:09,286] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708195.1_ASM2870819v1_genomic.fna/markers.fasta)
[2023-06-17 07:32:09,286] [INFO] Task started: Blastn
[2023-06-17 07:32:09,287] [INFO] Running command: blastn -query GCA_028708195.1_ASM2870819v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd7ee1ab-0632-469c-b61f-b63bbaf41902/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708195.1_ASM2870819v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 07:32:10,239] [INFO] Task succeeded: Blastn
[2023-06-17 07:32:10,244] [INFO] Selected 9 target genomes.
[2023-06-17 07:32:10,245] [INFO] Target genome list was writen to GCA_028708195.1_ASM2870819v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 07:32:10,247] [INFO] Task started: fastANI
[2023-06-17 07:32:10,248] [INFO] Running command: fastANI --query /var/lib/cwl/stg826d1ea7-d4ed-4fb4-906c-4b64dbe072d8/GCA_028708195.1_ASM2870819v1_genomic.fna.gz --refList GCA_028708195.1_ASM2870819v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708195.1_ASM2870819v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 07:32:15,533] [INFO] Task succeeded: fastANI
[2023-06-17 07:32:15,546] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 07:32:15,546] [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_014202345.1	s__Desulfovibrio intestinalis	86.561	524	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002237645.1	s__Desulfovibrio sp002237645	83.6922	486	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902702915.1	s__Desulfovibrio sp900095395	83.5489	494	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.97	99.97	0.99	0.99	2	-
GCF_000022125.1	s__Desulfovibrio desulfuricans_A	81.2018	398	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.36	99.22	0.93	0.89	5	-
GCA_905214305.1	s__Desulfovibrio sp905214305	81.0438	387	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009929215.1	s__Desulfovibrio sp009929215	79.1709	280	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420465.1	s__Desulfovibrio desulfuricans	79.1166	298	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.33	95.61	0.91	0.89	6	-
GCA_009712225.1	s__Desulfovibrio sp009712225	78.9813	294	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910575755.1	s__Desulfovibrio sp910575755	78.0679	202	598	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 07:32:15,549] [INFO] GTDB search result was written to GCA_028708195.1_ASM2870819v1_genomic.fna/result_gtdb.tsv
[2023-06-17 07:32:15,549] [INFO] ===== GTDB Search completed =====
[2023-06-17 07:32:15,552] [INFO] DFAST_QC result json was written to GCA_028708195.1_ASM2870819v1_genomic.fna/dqc_result.json
[2023-06-17 07:32:15,552] [INFO] DFAST_QC completed!
[2023-06-17 07:32:15,553] [INFO] Total running time: 0h0m50s