[2024-01-24 12:52:23,270] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:23,272] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:23,272] [INFO] DQC Reference Directory: /var/lib/cwl/stg7982847e-fa50-4a18-af87-4f6c90573c84/dqc_reference
[2024-01-24 12:52:24,519] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:24,520] [INFO] Task started: Prodigal
[2024-01-24 12:52:24,520] [INFO] Running command: gunzip -c /var/lib/cwl/stgbfd20a53-762a-4d64-9ba5-9c45a1ad2e6b/GCF_007991175.1_ASM799117v1_genomic.fna.gz | prodigal -d GCF_007991175.1_ASM799117v1_genomic.fna/cds.fna -a GCF_007991175.1_ASM799117v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:34,799] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:34,800] [INFO] Task started: HMMsearch
[2024-01-24 12:52:34,800] [INFO] Running command: hmmsearch --tblout GCF_007991175.1_ASM799117v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7982847e-fa50-4a18-af87-4f6c90573c84/dqc_reference/reference_markers.hmm GCF_007991175.1_ASM799117v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:35,141] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:35,142] [INFO] Found 6/6 markers.
[2024-01-24 12:52:35,180] [INFO] Query marker FASTA was written to GCF_007991175.1_ASM799117v1_genomic.fna/markers.fasta
[2024-01-24 12:52:35,180] [INFO] Task started: Blastn
[2024-01-24 12:52:35,181] [INFO] Running command: blastn -query GCF_007991175.1_ASM799117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7982847e-fa50-4a18-af87-4f6c90573c84/dqc_reference/reference_markers.fasta -out GCF_007991175.1_ASM799117v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:35,965] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:35,969] [INFO] Selected 11 target genomes.
[2024-01-24 12:52:35,970] [INFO] Target genome list was writen to GCF_007991175.1_ASM799117v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:36,007] [INFO] Task started: fastANI
[2024-01-24 12:52:36,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd20a53-762a-4d64-9ba5-9c45a1ad2e6b/GCF_007991175.1_ASM799117v1_genomic.fna.gz --refList GCF_007991175.1_ASM799117v1_genomic.fna/target_genomes.txt --output GCF_007991175.1_ASM799117v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:45,449] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:45,450] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7982847e-fa50-4a18-af87-4f6c90573c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:45,450] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7982847e-fa50-4a18-af87-4f6c90573c84/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:45,465] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:52:45,465] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:52:45,465] [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 boliviensis	strain=LC1	GCA_002265845.1	223527	223527	type	True	83.677	898	1220	95	below_threshold
Halomonas boliviensis	strain=LC1	GCA_000236035.1	223527	223527	type	True	83.5983	916	1220	95	below_threshold
Halomonas titanicae	strain=BH1	GCA_000336575.1	664683	664683	type	True	83.4156	928	1220	95	below_threshold
Halomonas sedimenti	strain=QX-2	GCA_013416325.1	2729618	2729618	type	True	83.278	900	1220	95	below_threshold
Halomonas glaciei	strain=DD39	GCA_013415125.1	186761	186761	type	True	82.827	821	1220	95	below_threshold
Halomonas maris	strain=QX-1	GCA_013371085.1	2729617	2729617	type	True	82.329	806	1220	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019504685.1	2852117	2852117	type	True	80.7614	642	1220	95	below_threshold
Halomonas profundi	strain=MT13	GCA_019722725.1	2852117	2852117	type	True	80.7552	665	1220	95	below_threshold
Halomonas populi	strain=MC	GCA_003989825.1	2498858	2498858	type	True	79.442	454	1220	95	below_threshold
Halomonas sulfidoxydans	strain=MCCC 1A11059	GCA_017868775.1	2733484	2733484	type	True	77.7716	260	1220	95	below_threshold
Halomonas lysinitropha	strain=3(2)	GCA_902500215.1	2607506	2607506	type	True	77.728	211	1220	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:45,468] [INFO] DFAST Taxonomy check result was written to GCF_007991175.1_ASM799117v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:45,469] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:45,469] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:45,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7982847e-fa50-4a18-af87-4f6c90573c84/dqc_reference/checkm_data
[2024-01-24 12:52:45,471] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:45,515] [INFO] Task started: CheckM
[2024-01-24 12:52:45,515] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007991175.1_ASM799117v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007991175.1_ASM799117v1_genomic.fna/checkm_input GCF_007991175.1_ASM799117v1_genomic.fna/checkm_result
[2024-01-24 12:53:19,576] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:19,578] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:19,601] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:19,601] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:19,602] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007991175.1_ASM799117v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:19,602] [INFO] Task started: Blastn
[2024-01-24 12:53:19,602] [INFO] Running command: blastn -query GCF_007991175.1_ASM799117v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7982847e-fa50-4a18-af87-4f6c90573c84/dqc_reference/reference_markers_gtdb.fasta -out GCF_007991175.1_ASM799117v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:20,864] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:20,868] [INFO] Selected 14 target genomes.
[2024-01-24 12:53:20,868] [INFO] Target genome list was writen to GCF_007991175.1_ASM799117v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:20,904] [INFO] Task started: fastANI
[2024-01-24 12:53:20,905] [INFO] Running command: fastANI --query /var/lib/cwl/stgbfd20a53-762a-4d64-9ba5-9c45a1ad2e6b/GCF_007991175.1_ASM799117v1_genomic.fna.gz --refList GCF_007991175.1_ASM799117v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007991175.1_ASM799117v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:33,717] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:33,729] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:33,729] [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_007991175.1	s__Halomonas variabilis	100.0	1218	1220	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_002257525.1	s__Halomonas ventosae_B	83.8177	938	1220	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	83.5983	916	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001882345.1	s__Halomonas sp001882345	83.535	913	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002211105.1	s__Halomonas campaniensis_A	83.4304	873	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	98.13	98.13	0.90	0.90	2	-
GCF_000336575.1	s__Halomonas titanicae	83.4156	928	1220	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	83.4048	911	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.52	96.69	0.85	0.81	3	-
GCF_013416325.1	s__Halomonas sedimenti	83.2684	901	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.54	99.54	0.90	0.90	2	-
GCF_013415125.1	s__Halomonas glaciei	82.8248	821	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	97.36	97.36	0.86	0.86	2	-
GCF_000235725.1	s__Halomonas sp000235725	82.6228	777	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	95.32	95.32	0.80	0.80	2	-
GCA_001507855.1	s__Halomonas sp001507855	82.3937	717	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	99.98	99.98	0.98	0.98	2	-
GCF_013371085.1	s__Halomonas maris	82.329	806	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011050415.1	s__Halomonas sp011050415	81.4287	782	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	0.99	0.99	2	-
GCF_003031405.1	s__Halomonas sp003031405	79.5538	493	1220	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Pseudomonadales;f__Halomonadaceae;g__Halomonas	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:33,731] [INFO] GTDB search result was written to GCF_007991175.1_ASM799117v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:33,732] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:33,737] [INFO] DFAST_QC result json was written to GCF_007991175.1_ASM799117v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:33,737] [INFO] DFAST_QC completed!
[2024-01-24 12:53:33,738] [INFO] Total running time: 0h1m10s