[2024-01-25 18:49:20,598] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:49:20,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:49:20,599] [INFO] DQC Reference Directory: /var/lib/cwl/stgecbe6f08-c828-4149-8578-4c984a1bf05f/dqc_reference
[2024-01-25 18:49:21,816] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:49:21,817] [INFO] Task started: Prodigal
[2024-01-25 18:49:21,817] [INFO] Running command: gunzip -c /var/lib/cwl/stg4acc5e84-a484-4659-ac29-c87c3918e69f/GCF_002952055.1_ASM295205v1_genomic.fna.gz | prodigal -d GCF_002952055.1_ASM295205v1_genomic.fna/cds.fna -a GCF_002952055.1_ASM295205v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:49:29,524] [INFO] Task succeeded: Prodigal
[2024-01-25 18:49:29,525] [INFO] Task started: HMMsearch
[2024-01-25 18:49:29,525] [INFO] Running command: hmmsearch --tblout GCF_002952055.1_ASM295205v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgecbe6f08-c828-4149-8578-4c984a1bf05f/dqc_reference/reference_markers.hmm GCF_002952055.1_ASM295205v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:49:29,729] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:49:29,730] [INFO] Found 6/6 markers.
[2024-01-25 18:49:29,753] [INFO] Query marker FASTA was written to GCF_002952055.1_ASM295205v1_genomic.fna/markers.fasta
[2024-01-25 18:49:29,753] [INFO] Task started: Blastn
[2024-01-25 18:49:29,753] [INFO] Running command: blastn -query GCF_002952055.1_ASM295205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecbe6f08-c828-4149-8578-4c984a1bf05f/dqc_reference/reference_markers.fasta -out GCF_002952055.1_ASM295205v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:49:30,306] [INFO] Task succeeded: Blastn
[2024-01-25 18:49:30,308] [INFO] Selected 17 target genomes.
[2024-01-25 18:49:30,309] [INFO] Target genome list was writen to GCF_002952055.1_ASM295205v1_genomic.fna/target_genomes.txt
[2024-01-25 18:49:30,325] [INFO] Task started: fastANI
[2024-01-25 18:49:30,325] [INFO] Running command: fastANI --query /var/lib/cwl/stg4acc5e84-a484-4659-ac29-c87c3918e69f/GCF_002952055.1_ASM295205v1_genomic.fna.gz --refList GCF_002952055.1_ASM295205v1_genomic.fna/target_genomes.txt --output GCF_002952055.1_ASM295205v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:49:42,721] [INFO] Task succeeded: fastANI
[2024-01-25 18:49:42,722] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgecbe6f08-c828-4149-8578-4c984a1bf05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:49:42,722] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgecbe6f08-c828-4149-8578-4c984a1bf05f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:49:42,728] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:49:42,728] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:49:42,728] [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
Desulfobulbus oralis	strain=HOT041/ORNL	GCA_002952055.1	1986146	1986146	type	True	100.0	924	924	95	conclusive
Desulfobulbus oligotrophicus	strain=Prop6	GCA_016446285.1	1909699	1909699	type	True	78.4241	58	924	95	below_threshold
Desulfobulbus elongatus	strain=DSM 2908	GCA_000621145.1	53332	53332	type	True	77.716	166	924	95	below_threshold
Desulfobulbus propionicus	strain=DSM 2032	GCA_000186885.1	894	894	type	True	77.4904	139	924	95	below_threshold
Desulfobulbus alkaliphilus	strain=DSM 24258	GCA_016918545.1	869814	869814	type	True	76.3044	69	924	95	below_threshold
Desulfogranum mediterraneum	strain=DSM 13871	GCA_000429965.1	160661	160661	type	True	76.1084	110	924	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:49:42,730] [INFO] DFAST Taxonomy check result was written to GCF_002952055.1_ASM295205v1_genomic.fna/tc_result.tsv
[2024-01-25 18:49:42,730] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:49:42,730] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:49:42,730] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgecbe6f08-c828-4149-8578-4c984a1bf05f/dqc_reference/checkm_data
[2024-01-25 18:49:42,731] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:49:42,760] [INFO] Task started: CheckM
[2024-01-25 18:49:42,760] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002952055.1_ASM295205v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002952055.1_ASM295205v1_genomic.fna/checkm_input GCF_002952055.1_ASM295205v1_genomic.fna/checkm_result
[2024-01-25 18:50:10,155] [INFO] Task succeeded: CheckM
[2024-01-25 18:50:10,156] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:50:10,175] [INFO] ===== Completeness check finished =====
[2024-01-25 18:50:10,175] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:50:10,176] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002952055.1_ASM295205v1_genomic.fna/markers.fasta)
[2024-01-25 18:50:10,176] [INFO] Task started: Blastn
[2024-01-25 18:50:10,176] [INFO] Running command: blastn -query GCF_002952055.1_ASM295205v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgecbe6f08-c828-4149-8578-4c984a1bf05f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002952055.1_ASM295205v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:50:10,991] [INFO] Task succeeded: Blastn
[2024-01-25 18:50:10,994] [INFO] Selected 19 target genomes.
[2024-01-25 18:50:10,994] [INFO] Target genome list was writen to GCF_002952055.1_ASM295205v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:50:11,011] [INFO] Task started: fastANI
[2024-01-25 18:50:11,011] [INFO] Running command: fastANI --query /var/lib/cwl/stg4acc5e84-a484-4659-ac29-c87c3918e69f/GCF_002952055.1_ASM295205v1_genomic.fna.gz --refList GCF_002952055.1_ASM295205v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002952055.1_ASM295205v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:50:22,446] [INFO] Task succeeded: fastANI
[2024-01-25 18:50:22,458] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:50:22,459] [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_002952055.1	s__Desulfobulbus oralis	100.0	924	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	98.11	98.11	0.97	0.97	2	conclusive
GCF_000621145.1	s__Desulfobulbus elongatus	77.6932	168	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000186885.1	s__Desulfobulbus propionicus	77.2586	137	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015484845.1	s__DRKI01 sp015484845	77.1953	121	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012744275.1	s__Desulfobulbus sp012744275	77.0838	156	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009782165.1	s__Desulfobulbus sp009782165	76.9218	88	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009778955.1	s__Desulfobulbus sp009778955	76.8217	90	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011051875.1	s__DRKI01 sp011051875	76.5277	86	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__DRKI01	95.0	99.14	99.09	0.93	0.90	3	-
GCA_009778235.1	s__Desulfobulbus sp009778235	76.5049	85	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001799275.1	s__YD12-FULL-57-12 sp001799275	76.4079	53	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__BM004;g__YD12-FULL-57-12	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016918545.1	s__Desulfobulbus alkaliphilus	76.3044	69	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903842475.1	s__Desulfobulbus sp903842475	76.2506	80	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfobulbaceae;g__Desulfobulbus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018830485.1	s__UBA2262 sp018830485	76.1126	61	924	d__Bacteria;p__Desulfobacterota;c__Desulfobulbia;o__Desulfobulbales;f__Desulfurivibrionaceae;g__UBA2262	95.0	99.86	99.86	0.95	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-25 18:50:22,463] [INFO] GTDB search result was written to GCF_002952055.1_ASM295205v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:50:22,463] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:50:22,469] [INFO] DFAST_QC result json was written to GCF_002952055.1_ASM295205v1_genomic.fna/dqc_result.json
[2024-01-25 18:50:22,469] [INFO] DFAST_QC completed!
[2024-01-25 18:50:22,469] [INFO] Total running time: 0h1m2s