[2024-01-24 10:47:09,684] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:09,687] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:09,687] [INFO] DQC Reference Directory: /var/lib/cwl/stg234ea572-15ff-40d7-a16f-19a59d8e9eda/dqc_reference
[2024-01-24 10:47:11,917] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:11,918] [INFO] Task started: Prodigal
[2024-01-24 10:47:11,918] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f58fe99-cadb-4ec8-9e42-550b061b394f/GCF_010499425.1_ASM1049942v1_genomic.fna.gz | prodigal -d GCF_010499425.1_ASM1049942v1_genomic.fna/cds.fna -a GCF_010499425.1_ASM1049942v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:25,020] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:25,020] [INFO] Task started: HMMsearch
[2024-01-24 10:47:25,021] [INFO] Running command: hmmsearch --tblout GCF_010499425.1_ASM1049942v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg234ea572-15ff-40d7-a16f-19a59d8e9eda/dqc_reference/reference_markers.hmm GCF_010499425.1_ASM1049942v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:25,291] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:25,293] [INFO] Found 6/6 markers.
[2024-01-24 10:47:25,329] [INFO] Query marker FASTA was written to GCF_010499425.1_ASM1049942v1_genomic.fna/markers.fasta
[2024-01-24 10:47:25,329] [INFO] Task started: Blastn
[2024-01-24 10:47:25,329] [INFO] Running command: blastn -query GCF_010499425.1_ASM1049942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg234ea572-15ff-40d7-a16f-19a59d8e9eda/dqc_reference/reference_markers.fasta -out GCF_010499425.1_ASM1049942v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:26,003] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:26,007] [INFO] Selected 12 target genomes.
[2024-01-24 10:47:26,007] [INFO] Target genome list was writen to GCF_010499425.1_ASM1049942v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:26,099] [INFO] Task started: fastANI
[2024-01-24 10:47:26,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f58fe99-cadb-4ec8-9e42-550b061b394f/GCF_010499425.1_ASM1049942v1_genomic.fna.gz --refList GCF_010499425.1_ASM1049942v1_genomic.fna/target_genomes.txt --output GCF_010499425.1_ASM1049942v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:35,958] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:35,959] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg234ea572-15ff-40d7-a16f-19a59d8e9eda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:35,959] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg234ea572-15ff-40d7-a16f-19a59d8e9eda/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:35,972] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:35,972] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:35,972] [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 sulfodismutans	strain=DSM 3696	GCA_010499425.1	63561	63561	type	True	100.0	1339	1349	95	conclusive
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	99.9934	1348	1349	95	conclusive
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	78.8114	504	1349	95	below_threshold
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	78.6731	505	1349	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	78.6629	477	1349	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	78.6233	487	1349	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	78.5558	502	1349	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	77.2815	292	1349	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	77.195	249	1349	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:35,975] [INFO] DFAST Taxonomy check result was written to GCF_010499425.1_ASM1049942v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:35,976] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:35,976] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:35,977] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg234ea572-15ff-40d7-a16f-19a59d8e9eda/dqc_reference/checkm_data
[2024-01-24 10:47:35,978] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:36,022] [INFO] Task started: CheckM
[2024-01-24 10:47:36,022] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010499425.1_ASM1049942v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010499425.1_ASM1049942v1_genomic.fna/checkm_input GCF_010499425.1_ASM1049942v1_genomic.fna/checkm_result
[2024-01-24 10:48:16,135] [INFO] Task succeeded: CheckM
[2024-01-24 10:48:16,136] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:48:16,162] [INFO] ===== Completeness check finished =====
[2024-01-24 10:48:16,162] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:48:16,162] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010499425.1_ASM1049942v1_genomic.fna/markers.fasta)
[2024-01-24 10:48:16,163] [INFO] Task started: Blastn
[2024-01-24 10:48:16,163] [INFO] Running command: blastn -query GCF_010499425.1_ASM1049942v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg234ea572-15ff-40d7-a16f-19a59d8e9eda/dqc_reference/reference_markers_gtdb.fasta -out GCF_010499425.1_ASM1049942v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:48:17,291] [INFO] Task succeeded: Blastn
[2024-01-24 10:48:17,296] [INFO] Selected 16 target genomes.
[2024-01-24 10:48:17,297] [INFO] Target genome list was writen to GCF_010499425.1_ASM1049942v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:48:17,336] [INFO] Task started: fastANI
[2024-01-24 10:48:17,336] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f58fe99-cadb-4ec8-9e42-550b061b394f/GCF_010499425.1_ASM1049942v1_genomic.fna.gz --refList GCF_010499425.1_ASM1049942v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010499425.1_ASM1049942v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:29,442] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:29,454] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:29,455] [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_013376455.1	s__Desulfolutivibrio sulfodismutans	99.9934	1348	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_013376475.1	s__Desulfolutivibrio sulfoxidireducens	84.2229	926	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.21	99.21	0.94	0.94	2	-
GCA_002482565.1	s__Solidesulfovibrio magneticus_B	78.8346	450	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004135975.1	s__Solidesulfovibrio carbinolicus	78.8206	504	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000307955.1	s__Solidesulfovibrio magneticus_A	78.8199	466	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702665.1	s__Solidesulfovibrio alcoholivorans	78.6439	479	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000179555.1	s__Solidesulfovibrio fructosivorans	78.6359	486	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177215.2	s__Solidesulfovibrio carbinoliphilus	78.581	497	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000245055.1	s__Solidesulfovibrio sp000245055	78.5443	499	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003525525.1	s__Solidesulfovibrio sp003525525	78.2197	317	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002382645.1	s__Aminidesulfovibrio sp002382645	78.1027	317	1349	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_000176915.2	s__Pseudodesulfovibrio aespoeensis	77.1646	252	1349	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Pseudodesulfovibrio	95.0	99.98	99.94	1.00	0.98	8	-
--------------------------------------------------------------------------------
[2024-01-24 10:48:29,456] [INFO] GTDB search result was written to GCF_010499425.1_ASM1049942v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:29,457] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:29,460] [INFO] DFAST_QC result json was written to GCF_010499425.1_ASM1049942v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:29,460] [INFO] DFAST_QC completed!
[2024-01-24 10:48:29,460] [INFO] Total running time: 0h1m20s