[2023-06-28 22:10:27,204] [INFO] DFAST_QC pipeline started.
[2023-06-28 22:10:27,208] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 22:10:27,208] [INFO] DQC Reference Directory: /var/lib/cwl/stg69c0ab57-6705-4495-90a6-2809733b049f/dqc_reference
[2023-06-28 22:10:28,468] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 22:10:28,469] [INFO] Task started: Prodigal
[2023-06-28 22:10:28,470] [INFO] Running command: gunzip -c /var/lib/cwl/stg57b217fb-6315-4d39-8a8f-4d18de15783c/GCA_944324545.1_BRZ_GG_bin126_genomic.fna.gz | prodigal -d GCA_944324545.1_BRZ_GG_bin126_genomic.fna/cds.fna -a GCA_944324545.1_BRZ_GG_bin126_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 22:10:36,607] [INFO] Task succeeded: Prodigal
[2023-06-28 22:10:36,608] [INFO] Task started: HMMsearch
[2023-06-28 22:10:36,608] [INFO] Running command: hmmsearch --tblout GCA_944324545.1_BRZ_GG_bin126_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg69c0ab57-6705-4495-90a6-2809733b049f/dqc_reference/reference_markers.hmm GCA_944324545.1_BRZ_GG_bin126_genomic.fna/protein.faa > /dev/null
[2023-06-28 22:10:36,842] [INFO] Task succeeded: HMMsearch
[2023-06-28 22:10:36,843] [INFO] Found 6/6 markers.
[2023-06-28 22:10:36,867] [INFO] Query marker FASTA was written to GCA_944324545.1_BRZ_GG_bin126_genomic.fna/markers.fasta
[2023-06-28 22:10:36,867] [INFO] Task started: Blastn
[2023-06-28 22:10:36,867] [INFO] Running command: blastn -query GCA_944324545.1_BRZ_GG_bin126_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c0ab57-6705-4495-90a6-2809733b049f/dqc_reference/reference_markers.fasta -out GCA_944324545.1_BRZ_GG_bin126_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:10:37,536] [INFO] Task succeeded: Blastn
[2023-06-28 22:10:37,540] [INFO] Selected 11 target genomes.
[2023-06-28 22:10:37,541] [INFO] Target genome list was writen to GCA_944324545.1_BRZ_GG_bin126_genomic.fna/target_genomes.txt
[2023-06-28 22:10:37,543] [INFO] Task started: fastANI
[2023-06-28 22:10:37,543] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b217fb-6315-4d39-8a8f-4d18de15783c/GCA_944324545.1_BRZ_GG_bin126_genomic.fna.gz --refList GCA_944324545.1_BRZ_GG_bin126_genomic.fna/target_genomes.txt --output GCA_944324545.1_BRZ_GG_bin126_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 22:10:44,446] [INFO] Task succeeded: fastANI
[2023-06-28 22:10:44,447] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg69c0ab57-6705-4495-90a6-2809733b049f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 22:10:44,447] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg69c0ab57-6705-4495-90a6-2809733b049f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 22:10:44,458] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 22:10:44,458] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 22:10:44,458] [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 piger	strain=ATCC 29098	GCA_000156375.1	901	901	suspected-type	True	80.0792	404	837	95	below_threshold
Desulfovibrio porci	strain=PG-178-WT-4	GCA_009696265.1	2605782	2605782	type	True	79.6066	423	837	95	below_threshold
Desulfovibrio legallii	strain=H1T	GCA_004309735.1	571438	571438	type	True	79.0647	301	837	95	below_threshold
Cupidesulfovibrio liaohensis	strain=XJ01	GCA_011682075.1	2604158	2604158	type	True	77.8799	185	837	95	below_threshold
Desulfovibrio intestinalis	strain=DSM 11275	GCA_014202345.1	58621	58621	type	True	77.7425	210	837	95	below_threshold
Cupidesulfovibrio termitidis	strain=HI1	GCA_000504305.1	42252	42252	type	True	77.3845	230	837	95	below_threshold
Bilophila wadsworthia	strain=ATCC 49260	GCA_000701705.1	35833	35833	type	True	77.2627	159	837	95	below_threshold
Megalodesulfovibrio gigas	strain=DSM 1382	GCA_000429285.1	879	879	type	True	76.9427	121	837	95	below_threshold
Megalodesulfovibrio gigas	strain=ATCC 19364	GCA_000468495.1	879	879	type	True	76.9329	125	837	95	below_threshold
Desulfovibrio vulgaris	strain=Hildenborough	GCA_000195755.1	881	881	type	True	76.9256	120	837	95	below_threshold
Pseudodesulfovibrio aespoeensis	strain=Aspo-2	GCA_000176915.2	182210	182210	type	True	76.6391	103	837	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 22:10:44,474] [INFO] DFAST Taxonomy check result was written to GCA_944324545.1_BRZ_GG_bin126_genomic.fna/tc_result.tsv
[2023-06-28 22:10:44,475] [INFO] ===== Taxonomy check completed =====
[2023-06-28 22:10:44,475] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 22:10:44,475] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg69c0ab57-6705-4495-90a6-2809733b049f/dqc_reference/checkm_data
[2023-06-28 22:10:44,478] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 22:10:44,512] [INFO] Task started: CheckM
[2023-06-28 22:10:44,512] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_944324545.1_BRZ_GG_bin126_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_944324545.1_BRZ_GG_bin126_genomic.fna/checkm_input GCA_944324545.1_BRZ_GG_bin126_genomic.fna/checkm_result
[2023-06-28 22:11:14,662] [INFO] Task succeeded: CheckM
[2023-06-28 22:11:14,663] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 22:11:14,684] [INFO] ===== Completeness check finished =====
[2023-06-28 22:11:14,685] [INFO] ===== Start GTDB Search =====
[2023-06-28 22:11:14,685] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_944324545.1_BRZ_GG_bin126_genomic.fna/markers.fasta)
[2023-06-28 22:11:14,686] [INFO] Task started: Blastn
[2023-06-28 22:11:14,686] [INFO] Running command: blastn -query GCA_944324545.1_BRZ_GG_bin126_genomic.fna/markers.fasta -db /var/lib/cwl/stg69c0ab57-6705-4495-90a6-2809733b049f/dqc_reference/reference_markers_gtdb.fasta -out GCA_944324545.1_BRZ_GG_bin126_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 22:11:15,723] [INFO] Task succeeded: Blastn
[2023-06-28 22:11:15,728] [INFO] Selected 13 target genomes.
[2023-06-28 22:11:15,729] [INFO] Target genome list was writen to GCA_944324545.1_BRZ_GG_bin126_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 22:11:15,730] [INFO] Task started: fastANI
[2023-06-28 22:11:15,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg57b217fb-6315-4d39-8a8f-4d18de15783c/GCA_944324545.1_BRZ_GG_bin126_genomic.fna.gz --refList GCA_944324545.1_BRZ_GG_bin126_genomic.fna/target_genomes_gtdb.txt --output GCA_944324545.1_BRZ_GG_bin126_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 22:11:23,645] [INFO] Task succeeded: fastANI
[2023-06-28 22:11:23,660] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-28 22:11:23,660] [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_019118345.1	s__Desulfovibrio intestinavium	99.5926	772	837	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_019118745.1	s__Desulfovibrio gallistercoris	84.5023	633	837	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_900116045.1	s__Desulfovibrio piger_A	80.2541	417	837	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.11	98.95	0.94	0.93	3	-
GCF_000156375.1	s__Desulfovibrio piger	80.052	406	837	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	99.18	98.09	0.98	0.96	5	-
GCF_012843875.1	s__Desulfovibrio sp900556755	80.0094	392	837	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0439	98.27	96.78	0.88	0.81	10	-
GCF_009696265.1	s__Desulfovibrio porci	79.6263	421	837	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.64	99.64	0.91	0.91	2	-
GCA_015062205.1	s__Desulfovibrio desulfuricans_D	79.6131	334	837	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_001553605.1	s__Desulfovibrio fairfieldensis	79.5663	410	837	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	97.09	95.23	0.86	0.83	6	-
GCA_019114565.1	s__Desulfovibrio intestinigallinarum	79.4232	347	837	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	79.3612	367	837	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_900547595.1	s__Desulfovibrio sp900547595	78.9967	276	837	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_900102485.1	s__Desulfovibrio legallii_A	78.9957	356	837	d__Bacteria;p__Desulfobacterota_I;c__Desulfovibrionia;o__Desulfovibrionales;f__Desulfovibrionaceae;g__Desulfovibrio	95.0	99.86	99.86	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-28 22:11:23,663] [INFO] GTDB search result was written to GCA_944324545.1_BRZ_GG_bin126_genomic.fna/result_gtdb.tsv
[2023-06-28 22:11:23,663] [INFO] ===== GTDB Search completed =====
[2023-06-28 22:11:23,667] [INFO] DFAST_QC result json was written to GCA_944324545.1_BRZ_GG_bin126_genomic.fna/dqc_result.json
[2023-06-28 22:11:23,667] [INFO] DFAST_QC completed!
[2023-06-28 22:11:23,667] [INFO] Total running time: 0h0m56s