[2023-06-17 01:28:51,908] [INFO] DFAST_QC pipeline started.
[2023-06-17 01:28:51,910] [INFO] DFAST_QC version: 0.5.7
[2023-06-17 01:28:51,911] [INFO] DQC Reference Directory: /var/lib/cwl/stg6dad5743-9f10-4147-8309-dec6e1250e15/dqc_reference
[2023-06-17 01:28:53,183] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-17 01:28:53,184] [INFO] Task started: Prodigal
[2023-06-17 01:28:53,184] [INFO] Running command: gunzip -c /var/lib/cwl/stg417794f1-01d1-4494-a3a8-569a6b89a970/GCA_009929795.1_ASM992979v1_genomic.fna.gz | prodigal -d GCA_009929795.1_ASM992979v1_genomic.fna/cds.fna -a GCA_009929795.1_ASM992979v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-17 01:29:01,604] [INFO] Task succeeded: Prodigal
[2023-06-17 01:29:01,605] [INFO] Task started: HMMsearch
[2023-06-17 01:29:01,605] [INFO] Running command: hmmsearch --tblout GCA_009929795.1_ASM992979v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6dad5743-9f10-4147-8309-dec6e1250e15/dqc_reference/reference_markers.hmm GCA_009929795.1_ASM992979v1_genomic.fna/protein.faa > /dev/null
[2023-06-17 01:29:01,966] [INFO] Task succeeded: HMMsearch
[2023-06-17 01:29:01,968] [INFO] Found 6/6 markers.
[2023-06-17 01:29:01,999] [INFO] Query marker FASTA was written to GCA_009929795.1_ASM992979v1_genomic.fna/markers.fasta
[2023-06-17 01:29:02,000] [INFO] Task started: Blastn
[2023-06-17 01:29:02,000] [INFO] Running command: blastn -query GCA_009929795.1_ASM992979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dad5743-9f10-4147-8309-dec6e1250e15/dqc_reference/reference_markers.fasta -out GCA_009929795.1_ASM992979v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:02,592] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:02,596] [INFO] Selected 26 target genomes.
[2023-06-17 01:29:02,597] [INFO] Target genome list was writen to GCA_009929795.1_ASM992979v1_genomic.fna/target_genomes.txt
[2023-06-17 01:29:02,635] [INFO] Task started: fastANI
[2023-06-17 01:29:02,636] [INFO] Running command: fastANI --query /var/lib/cwl/stg417794f1-01d1-4494-a3a8-569a6b89a970/GCA_009929795.1_ASM992979v1_genomic.fna.gz --refList GCA_009929795.1_ASM992979v1_genomic.fna/target_genomes.txt --output GCA_009929795.1_ASM992979v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-17 01:29:19,412] [INFO] Task succeeded: fastANI
[2023-06-17 01:29:19,412] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6dad5743-9f10-4147-8309-dec6e1250e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-17 01:29:19,412] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6dad5743-9f10-4147-8309-dec6e1250e15/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-17 01:29:19,425] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2023-06-17 01:29:19,426] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-17 01:29:19,426] [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
Desulfomicrobium baculatum	strain=DSM 4028	GCA_000023225.1	899	899	type	True	77.2306	105	848	95	below_threshold
Desulfomicrobium apsheronum	strain=DSM 5918	GCA_900114115.1	52560	52560	type	True	77.2084	114	848	95	below_threshold
Desulfomicrobium escambiense	strain=DSM 10707	GCA_000428825.1	29503	29503	type	True	77.0536	141	848	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_013376455.1	63561	63561	type	True	76.7571	115	848	95	below_threshold
Desulfovibrio sulfodismutans	strain=DSM 3696	GCA_010499425.1	63561	63561	type	True	76.7351	110	848	95	below_threshold
Solidesulfovibrio fructosivorans	strain=JJ	GCA_000179555.1	878	878	type	True	76.6091	92	848	95	below_threshold
Fundidesulfovibrio magnetotacticus	strain=FSS-1	GCA_013019105.1	2730080	2730080	type	True	76.5254	90	848	95	below_threshold
Pseudodesulfovibrio mercurii	strain=ND132	GCA_000189295.2	641491	641491	type	True	76.5086	124	848	95	below_threshold
Desulfovibrio carbinoliphilus subsp. oakridgensis	strain=FW-101-2B	GCA_000177215.2	694327	345370	type	True	76.4558	108	848	95	below_threshold
Pseudodesulfovibrio tunisiensis	strain=RB22	GCA_022809775.1	463192	463192	type	True	76.3042	65	848	95	below_threshold
Solidesulfovibrio alcoholivorans	strain=DSM 5433	GCA_000702665.1	81406	81406	type	True	76.2515	95	848	95	below_threshold
Desulfoplanes formicivorans	strain=Pf12B	GCA_001748225.1	1592317	1592317	type	True	76.2267	77	848	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-17 01:29:19,437] [INFO] DFAST Taxonomy check result was written to GCA_009929795.1_ASM992979v1_genomic.fna/tc_result.tsv
[2023-06-17 01:29:19,438] [INFO] ===== Taxonomy check completed =====
[2023-06-17 01:29:19,438] [INFO] ===== Start completeness check using CheckM =====
[2023-06-17 01:29:19,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6dad5743-9f10-4147-8309-dec6e1250e15/dqc_reference/checkm_data
[2023-06-17 01:29:19,440] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-17 01:29:19,479] [INFO] Task started: CheckM
[2023-06-17 01:29:19,480] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_009929795.1_ASM992979v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_009929795.1_ASM992979v1_genomic.fna/checkm_input GCA_009929795.1_ASM992979v1_genomic.fna/checkm_result
[2023-06-17 01:29:50,039] [INFO] Task succeeded: CheckM
[2023-06-17 01:29:50,042] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-17 01:29:50,065] [INFO] ===== Completeness check finished =====
[2023-06-17 01:29:50,066] [INFO] ===== Start GTDB Search =====
[2023-06-17 01:29:50,066] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_009929795.1_ASM992979v1_genomic.fna/markers.fasta)
[2023-06-17 01:29:50,067] [INFO] Task started: Blastn
[2023-06-17 01:29:50,067] [INFO] Running command: blastn -query GCA_009929795.1_ASM992979v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6dad5743-9f10-4147-8309-dec6e1250e15/dqc_reference/reference_markers_gtdb.fasta -out GCA_009929795.1_ASM992979v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-17 01:29:50,841] [INFO] Task succeeded: Blastn
[2023-06-17 01:29:50,845] [INFO] Selected 25 target genomes.
[2023-06-17 01:29:50,846] [INFO] Target genome list was writen to GCA_009929795.1_ASM992979v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-17 01:29:50,876] [INFO] Task started: fastANI
[2023-06-17 01:29:50,876] [INFO] Running command: fastANI --query /var/lib/cwl/stg417794f1-01d1-4494-a3a8-569a6b89a970/GCA_009929795.1_ASM992979v1_genomic.fna.gz --refList GCA_009929795.1_ASM992979v1_genomic.fna/target_genomes_gtdb.txt --output GCA_009929795.1_ASM992979v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-17 01:30:05,429] [INFO] Task succeeded: fastANI
[2023-06-17 01:30:05,446] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-17 01:30:05,446] [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_009929795.1	s__RZZR01 sp009929795	99.9999	844	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__RZZR01;g__RZZR01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003542385.1	s__Desulfomicrobium sp003542385	77.2568	107	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000428825.1	s__Desulfomicrobium escambiense	77.0351	142	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015709205.1	s__JACCQO01 sp015709205	76.96	117	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__JACCQO01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014873765.1	s__Desulfomicrobium macestii	76.9546	125	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfomicrobiaceae;g__Desulfomicrobium	95.0	98.27	98.27	0.85	0.85	2	-
GCF_013376455.1	s__Desulfolutivibrio sulfodismutans	76.7571	115	848	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_000179555.1	s__Solidesulfovibrio fructosivorans	76.586	93	848	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_000519125.1	s__Desulfocurvus vexinensis	76.5595	132	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfocurvus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013376475.1	s__Desulfolutivibrio sulfoxidireducens	76.5196	135	848	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_002382645.1	s__Aminidesulfovibrio sp002382645	76.5156	129	848	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_000526455.1	s__Solidesulfovibrio magneticus_C	76.4524	94	848	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_008830225.1	s__Pseudodesulfovibrio senegalensis	76.3681	51	848	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_013085545.1	s__Desulfovibrio_R marinus	76.3533	94	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio_R	95.0	99.02	99.02	0.95	0.95	2	-
GCA_015709315.1	s__Pseudodesulfovibrio sp015709315	76.2736	100	848	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_007625075.1	s__Desulfovibrio_R indonesiensis	76.2606	63	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio_R	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001748225.1	s__Desulfoplanes formicivorans	76.2267	77	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfoplanaceae;g__Desulfoplanes	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009856865.1	s__Solidesulfovibrio aerotolerans	76.0708	70	848	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Solidesulfovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-17 01:30:05,449] [INFO] GTDB search result was written to GCA_009929795.1_ASM992979v1_genomic.fna/result_gtdb.tsv
[2023-06-17 01:30:05,449] [INFO] ===== GTDB Search completed =====
[2023-06-17 01:30:05,453] [INFO] DFAST_QC result json was written to GCA_009929795.1_ASM992979v1_genomic.fna/dqc_result.json
[2023-06-17 01:30:05,453] [INFO] DFAST_QC completed!
[2023-06-17 01:30:05,453] [INFO] Total running time: 0h1m14s