[2024-01-25 18:40:05,554] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:40:05,556] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:40:05,556] [INFO] DQC Reference Directory: /var/lib/cwl/stg41acbc18-74d4-4e85-95de-b577a9f77dbb/dqc_reference
[2024-01-25 18:40:06,720] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:40:06,721] [INFO] Task started: Prodigal
[2024-01-25 18:40:06,721] [INFO] Running command: gunzip -c /var/lib/cwl/stg43b0c199-f359-4fab-9809-a9c8bb5fa8c1/GCF_013371085.1_ASM1337108v1_genomic.fna.gz | prodigal -d GCF_013371085.1_ASM1337108v1_genomic.fna/cds.fna -a GCF_013371085.1_ASM1337108v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:17,322] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:17,322] [INFO] Task started: HMMsearch
[2024-01-25 18:40:17,322] [INFO] Running command: hmmsearch --tblout GCF_013371085.1_ASM1337108v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg41acbc18-74d4-4e85-95de-b577a9f77dbb/dqc_reference/reference_markers.hmm GCF_013371085.1_ASM1337108v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:17,564] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:17,565] [INFO] Found 6/6 markers.
[2024-01-25 18:40:17,602] [INFO] Query marker FASTA was written to GCF_013371085.1_ASM1337108v1_genomic.fna/markers.fasta
[2024-01-25 18:40:17,603] [INFO] Task started: Blastn
[2024-01-25 18:40:17,603] [INFO] Running command: blastn -query GCF_013371085.1_ASM1337108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41acbc18-74d4-4e85-95de-b577a9f77dbb/dqc_reference/reference_markers.fasta -out GCF_013371085.1_ASM1337108v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:18,313] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:18,317] [INFO] Selected 11 target genomes.
[2024-01-25 18:40:18,318] [INFO] Target genome list was writen to GCF_013371085.1_ASM1337108v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:18,335] [INFO] Task started: fastANI
[2024-01-25 18:40:18,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b0c199-f359-4fab-9809-a9c8bb5fa8c1/GCF_013371085.1_ASM1337108v1_genomic.fna.gz --refList GCF_013371085.1_ASM1337108v1_genomic.fna/target_genomes.txt --output GCF_013371085.1_ASM1337108v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:28,360] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:28,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg41acbc18-74d4-4e85-95de-b577a9f77dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:28,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg41acbc18-74d4-4e85-95de-b577a9f77dbb/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:28,369] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:28,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:28,369] [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 maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	100.0	1461	1466	95	conclusive
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	92.2103	1122	1466	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	85.0993	1008	1466	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	84.9542	1036	1466	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	84.0371	968	1466	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	84.0316	966	1466	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	81.3511	714	1466	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	81.2958	736	1466	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.4916	497	1466	95	below_threshold
Halomonas ethanolica	strain=MCCC 1A11081	GCA_021404305.1	2733486	2733486	type	True	77.4099	242	1466	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.3746	184	1466	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:28,371] [INFO] DFAST Taxonomy check result was written to GCF_013371085.1_ASM1337108v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:28,371] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:28,371] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:28,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg41acbc18-74d4-4e85-95de-b577a9f77dbb/dqc_reference/checkm_data
[2024-01-25 18:40:28,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:28,417] [INFO] Task started: CheckM
[2024-01-25 18:40:28,417] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_013371085.1_ASM1337108v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_013371085.1_ASM1337108v1_genomic.fna/checkm_input GCF_013371085.1_ASM1337108v1_genomic.fna/checkm_result
[2024-01-25 18:41:01,594] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:01,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:01,613] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:01,614] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:01,614] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_013371085.1_ASM1337108v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:01,614] [INFO] Task started: Blastn
[2024-01-25 18:41:01,614] [INFO] Running command: blastn -query GCF_013371085.1_ASM1337108v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg41acbc18-74d4-4e85-95de-b577a9f77dbb/dqc_reference/reference_markers_gtdb.fasta -out GCF_013371085.1_ASM1337108v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:02,879] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:02,882] [INFO] Selected 9 target genomes.
[2024-01-25 18:41:02,882] [INFO] Target genome list was writen to GCF_013371085.1_ASM1337108v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:02,887] [INFO] Task started: fastANI
[2024-01-25 18:41:02,888] [INFO] Running command: fastANI --query /var/lib/cwl/stg43b0c199-f359-4fab-9809-a9c8bb5fa8c1/GCF_013371085.1_ASM1337108v1_genomic.fna.gz --refList GCF_013371085.1_ASM1337108v1_genomic.fna/target_genomes_gtdb.txt --output GCF_013371085.1_ASM1337108v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:12,701] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:12,708] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:12,708] [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_013371085.1	s__Halomonas maris	100.0	1461	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000235725.1	s__Halomonas sp000235725	93.9513	1085	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCF_013415125.1	s__Halomonas glaciei	92.1874	1124	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCA_002366715.1	s__Halomonas sp002366715	87.5569	1061	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001882345.1	s__Halomonas sp001882345	85.1694	1008	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000336575.1	s__Halomonas titanicae	84.9542	1036	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.70	97.17	0.86	0.84	22	-
GCF_004364445.1	s__Halomonas alkaliantarctica	84.8096	1008	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_002257525.1	s__Halomonas ventosae_B	84.6344	1027	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.23	97.92	0.94	0.87	4	-
GCF_000236035.1	s__Halomonas boliviensis	84.0317	965	1466	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:12,709] [INFO] GTDB search result was written to GCF_013371085.1_ASM1337108v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:12,710] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:12,714] [INFO] DFAST_QC result json was written to GCF_013371085.1_ASM1337108v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:12,714] [INFO] DFAST_QC completed!
[2024-01-25 18:41:12,714] [INFO] Total running time: 0h1m7s