[2024-01-24 14:46:55,584] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:46:55,590] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:46:55,590] [INFO] DQC Reference Directory: /var/lib/cwl/stgc195b2db-65a0-41f8-9f40-83af11f4b454/dqc_reference
[2024-01-24 14:46:58,016] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:46:58,017] [INFO] Task started: Prodigal
[2024-01-24 14:46:58,017] [INFO] Running command: gunzip -c /var/lib/cwl/stgd3d489e9-ed55-4ce3-86f4-40629900ba7a/GCF_000196875.2_ASM19687v2_genomic.fna.gz | prodigal -d GCF_000196875.2_ASM19687v2_genomic.fna/cds.fna -a GCF_000196875.2_ASM19687v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:47:11,679] [INFO] Task succeeded: Prodigal
[2024-01-24 14:47:11,680] [INFO] Task started: HMMsearch
[2024-01-24 14:47:11,680] [INFO] Running command: hmmsearch --tblout GCF_000196875.2_ASM19687v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc195b2db-65a0-41f8-9f40-83af11f4b454/dqc_reference/reference_markers.hmm GCF_000196875.2_ASM19687v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:47:11,980] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:47:11,982] [INFO] Found 6/6 markers.
[2024-01-24 14:47:12,031] [INFO] Query marker FASTA was written to GCF_000196875.2_ASM19687v2_genomic.fna/markers.fasta
[2024-01-24 14:47:12,032] [INFO] Task started: Blastn
[2024-01-24 14:47:12,032] [INFO] Running command: blastn -query GCF_000196875.2_ASM19687v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc195b2db-65a0-41f8-9f40-83af11f4b454/dqc_reference/reference_markers.fasta -out GCF_000196875.2_ASM19687v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:47:12,971] [INFO] Task succeeded: Blastn
[2024-01-24 14:47:12,975] [INFO] Selected 12 target genomes.
[2024-01-24 14:47:12,976] [INFO] Target genome list was writen to GCF_000196875.2_ASM19687v2_genomic.fna/target_genomes.txt
[2024-01-24 14:47:12,981] [INFO] Task started: fastANI
[2024-01-24 14:47:12,982] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3d489e9-ed55-4ce3-86f4-40629900ba7a/GCF_000196875.2_ASM19687v2_genomic.fna.gz --refList GCF_000196875.2_ASM19687v2_genomic.fna/target_genomes.txt --output GCF_000196875.2_ASM19687v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:47:24,152] [INFO] Task succeeded: fastANI
[2024-01-24 14:47:24,153] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc195b2db-65a0-41f8-9f40-83af11f4b454/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:47:24,154] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc195b2db-65a0-41f8-9f40-83af11f4b454/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:47:24,167] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:47:24,168] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:47:24,168] [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
Halomonas elongata	strain=type strain: DSM 2581	GCA_000196875.2	2746	2746	type	True	100.0	1353	1353	95	conclusive
Halomonas caseinilytica	strain=CGMCC 1.6773	GCA_900109905.1	438744	438744	type	True	88.7152	1012	1353	95	below_threshold
Halomonas caseinilytica	strain=JCM 14802	GCA_001662305.1	438744	438744	type	True	88.7005	1013	1353	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	83.4348	816	1353	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	83.3951	738	1353	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	83.1285	791	1353	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	81.4116	640	1353	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	81.2925	634	1353	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	81.0461	712	1353	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	80.6946	652	1353	95	below_threshold
Halomonas kenyensis	strain=DSM 17331	GCA_022341445.1	321266	321266	type	True	80.5458	590	1353	95	below_threshold
Chromohalobacter japonicus	strain=CECT 7219	GCA_023061175.1	223900	223900	type	True	79.7354	426	1353	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:47:24,173] [INFO] DFAST Taxonomy check result was written to GCF_000196875.2_ASM19687v2_genomic.fna/tc_result.tsv
[2024-01-24 14:47:24,173] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:47:24,173] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:47:24,174] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc195b2db-65a0-41f8-9f40-83af11f4b454/dqc_reference/checkm_data
[2024-01-24 14:47:24,175] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:47:24,215] [INFO] Task started: CheckM
[2024-01-24 14:47:24,216] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000196875.2_ASM19687v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000196875.2_ASM19687v2_genomic.fna/checkm_input GCF_000196875.2_ASM19687v2_genomic.fna/checkm_result
[2024-01-24 14:48:10,244] [INFO] Task succeeded: CheckM
[2024-01-24 14:48:10,245] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:48:10,273] [INFO] ===== Completeness check finished =====
[2024-01-24 14:48:10,273] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:48:10,274] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000196875.2_ASM19687v2_genomic.fna/markers.fasta)
[2024-01-24 14:48:10,274] [INFO] Task started: Blastn
[2024-01-24 14:48:10,274] [INFO] Running command: blastn -query GCF_000196875.2_ASM19687v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgc195b2db-65a0-41f8-9f40-83af11f4b454/dqc_reference/reference_markers_gtdb.fasta -out GCF_000196875.2_ASM19687v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:48:11,812] [INFO] Task succeeded: Blastn
[2024-01-24 14:48:11,816] [INFO] Selected 10 target genomes.
[2024-01-24 14:48:11,816] [INFO] Target genome list was writen to GCF_000196875.2_ASM19687v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:48:11,838] [INFO] Task started: fastANI
[2024-01-24 14:48:11,839] [INFO] Running command: fastANI --query /var/lib/cwl/stgd3d489e9-ed55-4ce3-86f4-40629900ba7a/GCF_000196875.2_ASM19687v2_genomic.fna.gz --refList GCF_000196875.2_ASM19687v2_genomic.fna/target_genomes_gtdb.txt --output GCF_000196875.2_ASM19687v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:48:21,201] [INFO] Task succeeded: fastANI
[2024-01-24 14:48:21,215] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:48:21,215] [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_000196875.2	s__Halomonas elongata	100.0	1353	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.75	98.56	0.95	0.92	4	conclusive
GCF_008274785.1	s__Halomonas eurihalina	93.1844	1096	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001662305.1	s__Halomonas caseinilytica	88.7005	1013	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.18	98.28	0.94	0.89	6	-
GCF_014192275.1	s__Halomonas stenophila	83.4156	817	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000265245.1	s__Halomonas smyrnensis	83.3655	740	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.45	98.45	0.89	0.89	2	-
GCF_002549795.1	s__Halomonas beimenensis	83.1754	780	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003966155.1	s__Halomonas nitroreducens	83.1227	792	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009363755.1	s__Halomonas sp009363755	82.5185	721	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002179555.1	s__Salinicola salarius_A	79.0383	405	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Salinicola	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000213805.1	s__Pseudomonas_E fulva_B	77.2002	244	1353	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Pseudomonadaceae;g__Pseudomonas_E	95.0	96.53	96.12	0.92	0.90	6	-
--------------------------------------------------------------------------------
[2024-01-24 14:48:21,217] [INFO] GTDB search result was written to GCF_000196875.2_ASM19687v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:48:21,218] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:48:21,221] [INFO] DFAST_QC result json was written to GCF_000196875.2_ASM19687v2_genomic.fna/dqc_result.json
[2024-01-24 14:48:21,221] [INFO] DFAST_QC completed!
[2024-01-24 14:48:21,221] [INFO] Total running time: 0h1m26s