[2023-06-17 04:33:40,918] [INFO] DFAST_QC pipeline started.
[2023-06-17 04:33:40,920] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 04:33:40,921] [INFO] DQC Reference Directory: /var/lib/cwl/stg34d47bbb-c1d7-4d38-9c53-e38dda68f810/dqc_reference
[2023-06-17 04:33:42,375] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 04:33:42,377] [INFO] Task started: Prodigal
[2023-06-17 04:33:42,377] [INFO] Running command: gunzip -c /var/lib/cwl/stg46ec40c9-af56-4b5b-bc43-3efcd8726b62/GCA_028708865.1_ASM2870886v1_genomic.fna.gz | prodigal -d GCA_028708865.1_ASM2870886v1_genomic.fna/cds.fna -a GCA_028708865.1_ASM2870886v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 04:33:52,160] [INFO] Task succeeded: Prodigal
[2023-06-17 04:33:52,160] [INFO] Task started: HMMsearch
[2023-06-17 04:33:52,160] [INFO] Running command: hmmsearch --tblout GCA_028708865.1_ASM2870886v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg34d47bbb-c1d7-4d38-9c53-e38dda68f810/dqc_reference/reference_markers.hmm GCA_028708865.1_ASM2870886v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 04:33:52,464] [INFO] Task succeeded: HMMsearch
[2023-06-17 04:33:52,466] [INFO] Found 6/6 markers.
[2023-06-17 04:33:52,515] [INFO] Query marker FASTA was written to GCA_028708865.1_ASM2870886v1_genomic.fna/markers.fasta
[2023-06-17 04:33:52,515] [INFO] Task started: Blastn
[2023-06-17 04:33:52,516] [INFO] Running command: blastn -query GCA_028708865.1_ASM2870886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34d47bbb-c1d7-4d38-9c53-e38dda68f810/dqc_reference/reference_markers.fasta -out GCA_028708865.1_ASM2870886v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:33:53,292] [INFO] Task succeeded: Blastn
[2023-06-17 04:33:53,296] [INFO] Selected 12 target genomes.
[2023-06-17 04:33:53,296] [INFO] Target genome list was writen to GCA_028708865.1_ASM2870886v1_genomic.fna/target_genomes.txt
[2023-06-17 04:33:53,301] [INFO] Task started: fastANI
[2023-06-17 04:33:53,302] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ec40c9-af56-4b5b-bc43-3efcd8726b62/GCA_028708865.1_ASM2870886v1_genomic.fna.gz --refList GCA_028708865.1_ASM2870886v1_genomic.fna/target_genomes.txt --output GCA_028708865.1_ASM2870886v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 04:34:03,276] [INFO] Task succeeded: fastANI
[2023-06-17 04:34:03,276] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg34d47bbb-c1d7-4d38-9c53-e38dda68f810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 04:34:03,277] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg34d47bbb-c1d7-4d38-9c53-e38dda68f810/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 04:34:03,290] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 04:34:03,291] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 04:34:03,291] [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
Paucidesulfovibrio gracilis	strain=DSM 16080	GCA_900167125.1	47158	47158	type	True	81.4725	556	924	95	below_threshold
Paucidesulfovibrio longus	strain=DSM 6739	GCA_000420485.1	889	889	type	True	80.3509	544	924	95	below_threshold
Pseudodesulfovibrio hydrargyri	strain=BerOc1	GCA_001874525.1	2125990	2125990	type	True	77.6072	202	924	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	77.4703	202	924	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	77.124	191	924	95	below_threshold
Pseudodesulfovibrio cashew	strain=SRB007	GCA_009762795.1	2678688	2678688	type	True	77.0526	165	924	95	below_threshold
Desulfonatronum thiodismutans	strain=MLF-1	GCA_000717475.2	159290	159290	type	True	76.416	80	924	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	76.3716	122	924	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_010499425.1	63561	63561	type	True	76.3462	120	924	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	76.3129	106	924	95	below_threshold
Desulfonatronum lacustre	strain=DSM 10312	GCA_000519265.1	66849	66849	type	True	76.2812	80	924	95	below_threshold
Desulfonatronum thiosulfatophilum	strain=ASO4-2	GCA_900104215.1	617002	617002	type	True	75.5243	54	924	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 04:34:03,293] [INFO] DFAST Taxonomy check result was written to GCA_028708865.1_ASM2870886v1_genomic.fna/tc_result.tsv
[2023-06-17 04:34:03,294] [INFO] ===== Taxonomy check completed =====
[2023-06-17 04:34:03,294] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 04:34:03,294] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg34d47bbb-c1d7-4d38-9c53-e38dda68f810/dqc_reference/checkm_data
[2023-06-17 04:34:03,296] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 04:34:03,345] [INFO] Task started: CheckM
[2023-06-17 04:34:03,346] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_028708865.1_ASM2870886v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_028708865.1_ASM2870886v1_genomic.fna/checkm_input GCA_028708865.1_ASM2870886v1_genomic.fna/checkm_result
[2023-06-17 04:34:35,852] [INFO] Task succeeded: CheckM
[2023-06-17 04:34:35,854] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 04:34:35,886] [INFO] ===== Completeness check finished =====
[2023-06-17 04:34:35,887] [INFO] ===== Start GTDB Search =====
[2023-06-17 04:34:35,887] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_028708865.1_ASM2870886v1_genomic.fna/markers.fasta)
[2023-06-17 04:34:35,888] [INFO] Task started: Blastn
[2023-06-17 04:34:35,888] [INFO] Running command: blastn -query GCA_028708865.1_ASM2870886v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg34d47bbb-c1d7-4d38-9c53-e38dda68f810/dqc_reference/reference_markers_gtdb.fasta -out GCA_028708865.1_ASM2870886v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 04:34:36,954] [INFO] Task succeeded: Blastn
[2023-06-17 04:34:36,974] [INFO] Selected 14 target genomes.
[2023-06-17 04:34:36,974] [INFO] Target genome list was writen to GCA_028708865.1_ASM2870886v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 04:34:37,005] [INFO] Task started: fastANI
[2023-06-17 04:34:37,006] [INFO] Running command: fastANI --query /var/lib/cwl/stg46ec40c9-af56-4b5b-bc43-3efcd8726b62/GCA_028708865.1_ASM2870886v1_genomic.fna.gz --refList GCA_028708865.1_ASM2870886v1_genomic.fna/target_genomes_gtdb.txt --output GCA_028708865.1_ASM2870886v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 04:34:45,832] [INFO] Task succeeded: fastANI
[2023-06-17 04:34:45,847] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-17 04:34:45,847] [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_900167125.1	s__Paucidesulfovibrio gracilis	81.4762	556	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420485.1	s__Paucidesulfovibrio longus	80.3753	543	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Paucidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008001235.1	s__Pseudodesulfovibrio sp008001235	77.6332	214	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001874525.1	s__Pseudodesulfovibrio hydrargyri	77.607	202	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008830225.1	s__Pseudodesulfovibrio senegalensis	77.5461	184	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000189295.2	s__Pseudodesulfovibrio mercurii	77.4555	203	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000176915.2	s__Pseudodesulfovibrio aespoeensis	77.4005	180	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.98	99.94	1.00	0.98	8	-
GCA_002840405.1	s__Humidesulfovibrio sp002840405	77.3812	143	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Humidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382645.1	s__Aminidesulfovibrio sp002382645	77.341	185	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Aminidesulfovibrio	95.0	99.05	98.75	0.90	0.87	3	-
GCF_000422565.1	s__Aminidesulfovibrio aminophilus	77.2711	204	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Aminidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016932995.1	s__JAFGBU01 sp016932995	77.2013	137	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__JAFGBU01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009762795.1	s__Pseudodesulfovibrio cashew	77.0509	165	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376475.1	s__Desulfolutivibrio sulfoxidireducens	76.5245	112	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.21	99.21	0.94	0.94	2	-
GCF_013376455.1	s__Desulfolutivibrio sulfodismutans	76.3716	122	924	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.99	99.99	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2023-06-17 04:34:45,849] [INFO] GTDB search result was written to GCA_028708865.1_ASM2870886v1_genomic.fna/result_gtdb.tsv
[2023-06-17 04:34:45,850] [INFO] ===== GTDB Search completed =====
[2023-06-17 04:34:45,854] [INFO] DFAST_QC result json was written to GCA_028708865.1_ASM2870886v1_genomic.fna/dqc_result.json
[2023-06-17 04:34:45,854] [INFO] DFAST_QC completed!
[2023-06-17 04:34:45,854] [INFO] Total running time: 0h1m5s