[2024-01-24 14:23:20,379] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:23:20,381] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:23:20,382] [INFO] DQC Reference Directory: /var/lib/cwl/stg1fe29e77-8061-44f8-8702-dd69e4eb3d48/dqc_reference
[2024-01-24 14:23:21,731] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:23:21,732] [INFO] Task started: Prodigal
[2024-01-24 14:23:21,733] [INFO] Running command: gunzip -c /var/lib/cwl/stga1e26038-7b9f-4b5d-bfd4-cae03ae7013f/GCF_003202165.1_ASM320216v1_genomic.fna.gz | prodigal -d GCF_003202165.1_ASM320216v1_genomic.fna/cds.fna -a GCF_003202165.1_ASM320216v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:37,609] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:37,610] [INFO] Task started: HMMsearch
[2024-01-24 14:23:37,610] [INFO] Running command: hmmsearch --tblout GCF_003202165.1_ASM320216v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1fe29e77-8061-44f8-8702-dd69e4eb3d48/dqc_reference/reference_markers.hmm GCF_003202165.1_ASM320216v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:38,029] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:38,031] [INFO] Found 6/6 markers.
[2024-01-24 14:23:38,076] [INFO] Query marker FASTA was written to GCF_003202165.1_ASM320216v1_genomic.fna/markers.fasta
[2024-01-24 14:23:38,077] [INFO] Task started: Blastn
[2024-01-24 14:23:38,077] [INFO] Running command: blastn -query GCF_003202165.1_ASM320216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fe29e77-8061-44f8-8702-dd69e4eb3d48/dqc_reference/reference_markers.fasta -out GCF_003202165.1_ASM320216v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:39,165] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:39,170] [INFO] Selected 17 target genomes.
[2024-01-24 14:23:39,171] [INFO] Target genome list was writen to GCF_003202165.1_ASM320216v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:39,178] [INFO] Task started: fastANI
[2024-01-24 14:23:39,178] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e26038-7b9f-4b5d-bfd4-cae03ae7013f/GCF_003202165.1_ASM320216v1_genomic.fna.gz --refList GCF_003202165.1_ASM320216v1_genomic.fna/target_genomes.txt --output GCF_003202165.1_ASM320216v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:57,363] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:57,364] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1fe29e77-8061-44f8-8702-dd69e4eb3d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:57,364] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1fe29e77-8061-44f8-8702-dd69e4eb3d48/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:57,378] [INFO] Found 17 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:57,378] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:57,379] [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 heilongjiangensis	strain=9-2	GCA_003202165.1	1387883	1387883	type	True	100.0	1627	1634	95	conclusive
Halomonas heilongjiangensis	strain=DSM 26881	GCA_002879645.1	1387883	1387883	type	True	99.9614	1534	1634	95	conclusive
Halomonas campaniensis	strain=5AG	GCA_014193375.1	213554	213554	type	True	85.8875	952	1634	95	below_threshold
Halomonas ventosae	strain=CECT 5797	GCA_004363555.1	229007	229007	type	True	85.1379	917	1634	95	below_threshold
Halomonas denitrificans	strain=DSM 18045	GCA_003056305.1	370769	370769	type	True	85.1113	874	1634	95	below_threshold
Halomonas shengliensis	strain=CGMCC 1.6444	GCA_900104135.1	419597	419597	type	True	85.0084	837	1634	95	below_threshold
Halomonas aestuarii	strain=Hb3	GCA_001886615.1	1897729	1897729	type	True	84.6105	844	1634	95	below_threshold
Halomonas campisalis	strain=A4	GCA_022341425.1	74661	74661	type	True	84.5837	931	1634	95	below_threshold
Halomonas stenophila	strain=CECT 7744	GCA_014192275.1	795312	795312	type	True	84.4973	954	1634	95	below_threshold
Halomonas alimentaria	strain=DSM 15356	GCA_009902005.1	147248	147248	type	True	84.2922	756	1634	95	below_threshold
Halomonas lactosivorans	strain=KCTC 52281	GCA_003254665.1	2185141	2185141	type	True	84.2815	958	1634	95	below_threshold
Halomonas smyrnensis	strain=AAD6	GCA_000265245.2	720605	720605	type	True	84.079	748	1634	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	84.0647	977	1634	95	below_threshold
Halomonas nitroreducens	strain=11S	GCA_003966155.1	447425	447425	type	True	83.7679	922	1634	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	83.5659	821	1634	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	83.4615	923	1634	95	below_threshold
Halomonas tianxiuensis	strain=BC-M4-5	GCA_009834345.1	2497861	2497861	type	True	82.9809	1000	1634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:57,381] [INFO] DFAST Taxonomy check result was written to GCF_003202165.1_ASM320216v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:57,381] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:57,381] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:57,381] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1fe29e77-8061-44f8-8702-dd69e4eb3d48/dqc_reference/checkm_data
[2024-01-24 14:23:57,382] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:57,430] [INFO] Task started: CheckM
[2024-01-24 14:23:57,431] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003202165.1_ASM320216v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003202165.1_ASM320216v1_genomic.fna/checkm_input GCF_003202165.1_ASM320216v1_genomic.fna/checkm_result
[2024-01-24 14:24:46,778] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:46,779] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:46,806] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:46,807] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:46,807] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003202165.1_ASM320216v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:46,807] [INFO] Task started: Blastn
[2024-01-24 14:24:46,808] [INFO] Running command: blastn -query GCF_003202165.1_ASM320216v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1fe29e77-8061-44f8-8702-dd69e4eb3d48/dqc_reference/reference_markers_gtdb.fasta -out GCF_003202165.1_ASM320216v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:48,816] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:48,821] [INFO] Selected 15 target genomes.
[2024-01-24 14:24:48,821] [INFO] Target genome list was writen to GCF_003202165.1_ASM320216v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:48,837] [INFO] Task started: fastANI
[2024-01-24 14:24:48,837] [INFO] Running command: fastANI --query /var/lib/cwl/stga1e26038-7b9f-4b5d-bfd4-cae03ae7013f/GCF_003202165.1_ASM320216v1_genomic.fna.gz --refList GCF_003202165.1_ASM320216v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003202165.1_ASM320216v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:25:02,818] [INFO] Task succeeded: fastANI
[2024-01-24 14:25:02,831] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:25:02,831] [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_002879645.1	s__Halomonas heilongjiangensis	99.9614	1534	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	1.00	1.00	2	conclusive
GCF_003202205.1	s__Halomonas sp003202205	91.1144	1140	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014193375.1	s__Halomonas campaniensis	85.9006	950	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003182195.1	s__Halomonas sp003182195	85.2285	798	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.47	95.24	0.85	0.84	3	-
GCF_003056305.1	s__Halomonas denitrificans	85.148	871	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004363555.1	s__Halomonas ventosae	85.1356	918	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.59	95.59	0.89	0.89	2	-
GCF_900104135.1	s__Halomonas shengliensis	85.0083	837	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.66	95.66	0.79	0.79	2	-
GCF_009363755.1	s__Halomonas sp009363755	84.8849	869	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014859505.1	s__Halomonas sp014859505	84.8079	751	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886615.1	s__Halomonas aestuarii	84.6282	843	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004551485.1	s__Halomonas azerbaijanica	84.4533	960	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018401555.1	s__Halomonas sp018401555	84.4117	719	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003552795.1	s__Halomonas sp003552795	84.3269	609	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003254665.1	s__Halomonas lactosivorans	84.3146	954	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015992245.1	s__Halomonas sp015992245	84.114	974	1634	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.35	99.35	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:25:02,833] [INFO] GTDB search result was written to GCF_003202165.1_ASM320216v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:25:02,834] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:25:02,837] [INFO] DFAST_QC result json was written to GCF_003202165.1_ASM320216v1_genomic.fna/dqc_result.json
[2024-01-24 14:25:02,837] [INFO] DFAST_QC completed!
[2024-01-24 14:25:02,837] [INFO] Total running time: 0h1m42s