[2024-01-24 13:19:25,629] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:19:25,631] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:19:25,631] [INFO] DQC Reference Directory: /var/lib/cwl/stgcf1faf51-1fbe-46af-a3aa-30704f7b0c20/dqc_reference
[2024-01-24 13:19:26,898] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:19:26,899] [INFO] Task started: Prodigal
[2024-01-24 13:19:26,899] [INFO] Running command: gunzip -c /var/lib/cwl/stg3fcb0799-a33a-4df5-b496-9072ba85df86/GCF_013376475.1_ASM1337647v1_genomic.fna.gz | prodigal -d GCF_013376475.1_ASM1337647v1_genomic.fna/cds.fna -a GCF_013376475.1_ASM1337647v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:19:40,150] [INFO] Task succeeded: Prodigal
[2024-01-24 13:19:40,150] [INFO] Task started: HMMsearch
[2024-01-24 13:19:40,150] [INFO] Running command: hmmsearch --tblout GCF_013376475.1_ASM1337647v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcf1faf51-1fbe-46af-a3aa-30704f7b0c20/dqc_reference/reference_markers.hmm GCF_013376475.1_ASM1337647v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:19:40,383] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:19:40,384] [INFO] Found 6/6 markers.
[2024-01-24 13:19:40,418] [INFO] Query marker FASTA was written to GCF_013376475.1_ASM1337647v1_genomic.fna/markers.fasta
[2024-01-24 13:19:40,419] [INFO] Task started: Blastn
[2024-01-24 13:19:40,419] [INFO] Running command: blastn -query GCF_013376475.1_ASM1337647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf1faf51-1fbe-46af-a3aa-30704f7b0c20/dqc_reference/reference_markers.fasta -out GCF_013376475.1_ASM1337647v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:41,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:41,090] [INFO] Selected 11 target genomes.
[2024-01-24 13:19:41,091] [INFO] Target genome list was writen to GCF_013376475.1_ASM1337647v1_genomic.fna/target_genomes.txt
[2024-01-24 13:19:41,094] [INFO] Task started: fastANI
[2024-01-24 13:19:41,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fcb0799-a33a-4df5-b496-9072ba85df86/GCF_013376475.1_ASM1337647v1_genomic.fna.gz --refList GCF_013376475.1_ASM1337647v1_genomic.fna/target_genomes.txt --output GCF_013376475.1_ASM1337647v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:19:50,080] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:50,081] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcf1faf51-1fbe-46af-a3aa-30704f7b0c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:19:50,081] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcf1faf51-1fbe-46af-a3aa-30704f7b0c20/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:19:50,090] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:19:50,090] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:19:50,090] [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	84.1515	930	1385	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	84.1386	977	1385	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	78.9605	519	1385	95	below_threshold
Solidesulfovibrio magneticus	strain=RS-1	GCA_000010665.1	184917	184917	type	True	78.9039	499	1385	95	below_threshold
Solidesulfovibrio carbinolicus	strain=DSM 3852	GCA_004135975.1	296842	296842	type	True	78.8837	498	1385	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	78.837	494	1385	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	78.7692	511	1385	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	78.0045	405	1385	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	77.297	251	1385	95	below_threshold
Desulfonatronum thioautotrophicum	strain=ASO4-1	GCA_000934745.1	617001	617001	type	True	76.4215	108	1385	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:19:50,092] [INFO] DFAST Taxonomy check result was written to GCF_013376475.1_ASM1337647v1_genomic.fna/tc_result.tsv
[2024-01-24 13:19:50,092] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:19:50,093] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:19:50,093] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcf1faf51-1fbe-46af-a3aa-30704f7b0c20/dqc_reference/checkm_data
[2024-01-24 13:19:50,094] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:19:50,132] [INFO] Task started: CheckM
[2024-01-24 13:19:50,133] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013376475.1_ASM1337647v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013376475.1_ASM1337647v1_genomic.fna/checkm_input GCF_013376475.1_ASM1337647v1_genomic.fna/checkm_result
[2024-01-24 13:20:29,400] [INFO] Task succeeded: CheckM
[2024-01-24 13:20:29,402] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:20:29,425] [INFO] ===== Completeness check finished =====
[2024-01-24 13:20:29,426] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:20:29,426] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013376475.1_ASM1337647v1_genomic.fna/markers.fasta)
[2024-01-24 13:20:29,426] [INFO] Task started: Blastn
[2024-01-24 13:20:29,426] [INFO] Running command: blastn -query GCF_013376475.1_ASM1337647v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcf1faf51-1fbe-46af-a3aa-30704f7b0c20/dqc_reference/reference_markers_gtdb.fasta -out GCF_013376475.1_ASM1337647v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:20:30,414] [INFO] Task succeeded: Blastn
[2024-01-24 13:20:30,423] [INFO] Selected 13 target genomes.
[2024-01-24 13:20:30,424] [INFO] Target genome list was writen to GCF_013376475.1_ASM1337647v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:20:30,441] [INFO] Task started: fastANI
[2024-01-24 13:20:30,441] [INFO] Running command: fastANI --query /var/lib/cwl/stg3fcb0799-a33a-4df5-b496-9072ba85df86/GCF_013376475.1_ASM1337647v1_genomic.fna.gz --refList GCF_013376475.1_ASM1337647v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013376475.1_ASM1337647v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:20:41,266] [INFO] Task succeeded: fastANI
[2024-01-24 13:20:41,277] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:20:41,277] [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_013376475.1	s__Desulfolutivibrio sulfoxidireducens	100.0	1384	1385	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.21	99.21	0.94	0.94	2	conclusive
GCF_013376455.1	s__Desulfolutivibrio sulfodismutans	84.1439	975	1385	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfolutivibrio	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000177215.2	s__Solidesulfovibrio carbinoliphilus	78.9687	518	1385	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	78.851	493	1385	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	78.7824	511	1385	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_002482565.1	s__Solidesulfovibrio magneticus_B	78.7207	456	1385	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	78.7032	536	1385	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	78.589	328	1385	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_001936595.1	s__Solidesulfovibrio sp001936595	78.1751	453	1385	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_000176915.2	s__Pseudodesulfovibrio aespoeensis	77.2665	255	1385	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_000403945.1	s__Desulfovibrio sp000403945	76.8681	69	1385	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_000934745.1	s__Desulfonatronum thioautotrophicum	76.4215	108	1385	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfonatronaceae;g__Desulfonatronum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000420465.1	s__Desulfovibrio desulfuricans	76.1998	53	1385	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	96.33	95.61	0.91	0.89	6	-
--------------------------------------------------------------------------------
[2024-01-24 13:20:41,279] [INFO] GTDB search result was written to GCF_013376475.1_ASM1337647v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:20:41,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:20:41,282] [INFO] DFAST_QC result json was written to GCF_013376475.1_ASM1337647v1_genomic.fna/dqc_result.json
[2024-01-24 13:20:41,283] [INFO] DFAST_QC completed!
[2024-01-24 13:20:41,283] [INFO] Total running time: 0h1m16s