[2024-01-24 13:17:15,630] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:15,632] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:15,632] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fb2a439-0d10-4a66-822d-5108dc0561da/dqc_reference
[2024-01-24 13:17:16,977] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:16,978] [INFO] Task started: Prodigal
[2024-01-24 13:17:16,979] [INFO] Running command: gunzip -c /var/lib/cwl/stg953345ba-2e42-4864-8223-3696770ff4ed/GCF_008064635.1_ASM806463v1_genomic.fna.gz | prodigal -d GCF_008064635.1_ASM806463v1_genomic.fna/cds.fna -a GCF_008064635.1_ASM806463v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:17:30,533] [INFO] Task succeeded: Prodigal
[2024-01-24 13:17:30,534] [INFO] Task started: HMMsearch
[2024-01-24 13:17:30,534] [INFO] Running command: hmmsearch --tblout GCF_008064635.1_ASM806463v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fb2a439-0d10-4a66-822d-5108dc0561da/dqc_reference/reference_markers.hmm GCF_008064635.1_ASM806463v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:17:30,804] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:17:30,806] [INFO] Found 6/6 markers.
[2024-01-24 13:17:30,915] [INFO] Query marker FASTA was written to GCF_008064635.1_ASM806463v1_genomic.fna/markers.fasta
[2024-01-24 13:17:30,915] [INFO] Task started: Blastn
[2024-01-24 13:17:30,915] [INFO] Running command: blastn -query GCF_008064635.1_ASM806463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fb2a439-0d10-4a66-822d-5108dc0561da/dqc_reference/reference_markers.fasta -out GCF_008064635.1_ASM806463v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:17:31,836] [INFO] Task succeeded: Blastn
[2024-01-24 13:17:31,845] [INFO] Selected 14 target genomes.
[2024-01-24 13:17:31,845] [INFO] Target genome list was writen to GCF_008064635.1_ASM806463v1_genomic.fna/target_genomes.txt
[2024-01-24 13:17:31,850] [INFO] Task started: fastANI
[2024-01-24 13:17:31,850] [INFO] Running command: fastANI --query /var/lib/cwl/stg953345ba-2e42-4864-8223-3696770ff4ed/GCF_008064635.1_ASM806463v1_genomic.fna.gz --refList GCF_008064635.1_ASM806463v1_genomic.fna/target_genomes.txt --output GCF_008064635.1_ASM806463v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:17:43,513] [INFO] Task succeeded: fastANI
[2024-01-24 13:17:43,514] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fb2a439-0d10-4a66-822d-5108dc0561da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:17:43,514] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fb2a439-0d10-4a66-822d-5108dc0561da/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:17:43,532] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:17:43,532] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:17:43,532] [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
Parahaliea aestuarii	strain=S2-26	GCA_008064635.1	1852021	1852021	type	True	100.0	1476	1478	95	conclusive
Parahaliea mediterranea	strain=DSM 21924	GCA_003402235.1	651086	651086	type	True	85.0859	1100	1478	95	below_threshold
Parahaliea maris	strain=HSLHS9	GCA_008064665.1	2716870	2716870	type	True	81.7691	813	1478	95	below_threshold
Seongchinamella sediminis	strain=U0301	GCA_003457605.1	2283635	2283635	type	True	78.9128	467	1478	95	below_threshold
Kineobactrum salinum	strain=M2	GCA_010669285.1	2708301	2708301	type	True	78.4121	385	1478	95	below_threshold
Seongchinamella unica	strain=GH4-78	GCA_004354085.1	2547392	2547392	type	True	78.2937	368	1478	95	below_threshold
Haliea salexigens	strain=DSM 19537	GCA_000423125.1	287487	287487	type	True	77.808	378	1478	95	below_threshold
Halioglobus japonicus	strain=NBRC 107739	GCA_001983995.1	930805	930805	type	True	77.4552	282	1478	95	below_threshold
Kineobactrum sediminis	strain=F02	GCA_002868715.1	1905677	1905677	type	True	77.2766	290	1478	95	below_threshold
Pseudomonas aeruginosa	strain=DSM 50071	GCA_024169805.1	287	287	type	True	77.0168	209	1478	95	below_threshold
Pseudomonas aeruginosa	strain=JCM 5962	GCA_022496575.1	287	287	type	True	76.9346	211	1478	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_022554105.1	86173	86173	type	True	76.6981	144	1478	95	below_threshold
Microbulbifer elongatus	strain=DSM 6810	GCA_021165935.1	86173	86173	type	True	76.6295	148	1478	95	below_threshold
Pseudomonas insulae	strain=UL073	GCA_016901015.1	2809017	2809017	type	True	76.616	204	1478	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:17:43,534] [INFO] DFAST Taxonomy check result was written to GCF_008064635.1_ASM806463v1_genomic.fna/tc_result.tsv
[2024-01-24 13:17:43,535] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:17:43,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:17:43,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fb2a439-0d10-4a66-822d-5108dc0561da/dqc_reference/checkm_data
[2024-01-24 13:17:43,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:17:43,585] [INFO] Task started: CheckM
[2024-01-24 13:17:43,585] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008064635.1_ASM806463v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008064635.1_ASM806463v1_genomic.fna/checkm_input GCF_008064635.1_ASM806463v1_genomic.fna/checkm_result
[2024-01-24 13:18:24,329] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:24,331] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:24,355] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:24,356] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:24,356] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008064635.1_ASM806463v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:24,357] [INFO] Task started: Blastn
[2024-01-24 13:18:24,357] [INFO] Running command: blastn -query GCF_008064635.1_ASM806463v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fb2a439-0d10-4a66-822d-5108dc0561da/dqc_reference/reference_markers_gtdb.fasta -out GCF_008064635.1_ASM806463v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:26,023] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:26,027] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:26,027] [INFO] Target genome list was writen to GCF_008064635.1_ASM806463v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:26,049] [INFO] Task started: fastANI
[2024-01-24 13:18:26,049] [INFO] Running command: fastANI --query /var/lib/cwl/stg953345ba-2e42-4864-8223-3696770ff4ed/GCF_008064635.1_ASM806463v1_genomic.fna.gz --refList GCF_008064635.1_ASM806463v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008064635.1_ASM806463v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:34,983] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:35,001] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:35,002] [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_008064635.1	s__Parahaliea aestuarii	100.0	1476	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003402235.1	s__Parahaliea mediterranea	85.0764	1101	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008064665.1	s__Parahaliea maris	81.784	811	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255185.1	s__Parahaliea mediterranea_A	81.2773	821	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Parahaliea	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004745945.1	s__Halioglobus sp004745945	79.3432	461	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003457605.1	s__Halioglobus sediminis	78.9227	466	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009937575.1	s__Halioglobus sp009937575	78.4314	333	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004354085.1	s__Halioglobus sp004354085	78.2934	368	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008370495.1	s__Halioglobus sp008370495	77.9447	302	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Halioglobus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002868715.1	s__Kineobactrum sediminis	77.2845	290	1478	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halieaceae;g__Kineobactrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:35,004] [INFO] GTDB search result was written to GCF_008064635.1_ASM806463v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:35,005] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:35,010] [INFO] DFAST_QC result json was written to GCF_008064635.1_ASM806463v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:35,010] [INFO] DFAST_QC completed!
[2024-01-24 13:18:35,010] [INFO] Total running time: 0h1m19s