[2024-01-24 13:25:47,596] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:47,599] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:47,600] [INFO] DQC Reference Directory: /var/lib/cwl/stgded33d7c-534a-4732-96fb-aca92169b02f/dqc_reference
[2024-01-24 13:25:48,964] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:48,965] [INFO] Task started: Prodigal
[2024-01-24 13:25:48,965] [INFO] Running command: gunzip -c /var/lib/cwl/stg836edb9b-4ae5-4aa5-a13c-f49dfb097f88/GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/cds.fna -a GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:26:06,360] [INFO] Task succeeded: Prodigal
[2024-01-24 13:26:06,361] [INFO] Task started: HMMsearch
[2024-01-24 13:26:06,361] [INFO] Running command: hmmsearch --tblout GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgded33d7c-534a-4732-96fb-aca92169b02f/dqc_reference/reference_markers.hmm GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:26:06,623] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:26:06,624] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg836edb9b-4ae5-4aa5-a13c-f49dfb097f88/GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna.gz]
[2024-01-24 13:26:06,657] [INFO] Query marker FASTA was written to GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 13:26:06,658] [INFO] Task started: Blastn
[2024-01-24 13:26:06,658] [INFO] Running command: blastn -query GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgded33d7c-534a-4732-96fb-aca92169b02f/dqc_reference/reference_markers.fasta -out GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:07,192] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:07,206] [INFO] Selected 12 target genomes.
[2024-01-24 13:26:07,207] [INFO] Target genome list was writen to GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 13:26:07,214] [INFO] Task started: fastANI
[2024-01-24 13:26:07,214] [INFO] Running command: fastANI --query /var/lib/cwl/stg836edb9b-4ae5-4aa5-a13c-f49dfb097f88/GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna.gz --refList GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:26:15,766] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:15,767] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgded33d7c-534a-4732-96fb-aca92169b02f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:26:15,767] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgded33d7c-534a-4732-96fb-aca92169b02f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:26:15,777] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:26:15,777] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:26:15,777] [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
Halovenus aranensis	strain=IBRC-M10015	GCA_900100385.1	890420	890420	type	True	100.0	1065	1070	95	conclusive
Halovenus carboxidivorans	strain=WSH3	GCA_009831575.1	2692199	2692199	type	True	77.787	288	1070	95	below_threshold
Halorientalis regularis	strain=TNN28	GCA_023698535.1	660518	660518	type	True	77.6123	244	1070	95	below_threshold
Halorientalis marina	strain=GDY88	GCA_023028345.1	2931976	2931976	type	True	77.5841	279	1070	95	below_threshold
Halomicrobium katesii	strain=DSM 19301	GCA_000379085.1	437163	437163	type	True	77.5649	243	1070	95	below_threshold
Halorientalis pallida	strain=F13-25	GCA_004118325.1	2479928	2479928	type	True	77.3221	242	1070	95	below_threshold
Halomicrobium mukohataei	strain=DSM 12286	GCA_000023965.1	57705	57705	type	True	77.291	247	1070	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	77.21	279	1070	95	below_threshold
Halorientalis brevis	strain=YC89	GCA_023077655.1	1126241	1126241	type	True	77.1088	239	1070	95	below_threshold
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	76.8808	202	1070	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	76.7541	192	1070	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	76.4864	193	1070	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:26:15,779] [INFO] DFAST Taxonomy check result was written to GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 13:26:15,780] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:26:15,780] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:26:15,780] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgded33d7c-534a-4732-96fb-aca92169b02f/dqc_reference/checkm_data
[2024-01-24 13:26:15,782] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:26:15,822] [INFO] Task started: CheckM
[2024-01-24 13:26:15,822] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/checkm_input GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 13:27:04,670] [INFO] Task succeeded: CheckM
[2024-01-24 13:27:04,672] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:27:04,696] [INFO] ===== Completeness check finished =====
[2024-01-24 13:27:04,697] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:27:04,697] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 13:27:04,698] [INFO] Task started: Blastn
[2024-01-24 13:27:04,698] [INFO] Running command: blastn -query GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgded33d7c-534a-4732-96fb-aca92169b02f/dqc_reference/reference_markers_gtdb.fasta -out GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:05,158] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:05,161] [INFO] Selected 11 target genomes.
[2024-01-24 13:27:05,161] [INFO] Target genome list was writen to GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:27:05,169] [INFO] Task started: fastANI
[2024-01-24 13:27:05,170] [INFO] Running command: fastANI --query /var/lib/cwl/stg836edb9b-4ae5-4aa5-a13c-f49dfb097f88/GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna.gz --refList GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:27:11,868] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:11,884] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:27:11,884] [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_900100385.1	s__Halovenus aranensis	100.0	1065	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003021285.1	s__Halovenus sp003021285	78.3664	260	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003551265.1	s__Halovenus sp003551265	77.9146	264	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003021015.1	s__Halovenus sp003021015	77.8656	288	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	96.48	96.48	0.87	0.87	2	-
GCA_003022725.1	s__Halovenus sp003022725	77.8192	279	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halovenus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000379085.1	s__Halomicrobium katesii	77.5638	244	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	96.8107	N/A	N/A	N/A	N/A	1	-
GCF_004118325.1	s__Halorientalis sp004118325	77.2958	245	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halorientalis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000023965.1	s__Halomicrobium mukohataei	77.2915	247	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halomicrobium	96.8107	100.00	100.00	1.00	1.00	4	-
GCA_003021655.1	s__QS-4-69-31 sp003021655	77.2624	225	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__QS-4-69-31	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	77.2005	280	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001485535.1	s__Halobacterium sp001485535	76.7749	199	1070	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Halobacteriaceae;g__Halobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:27:11,886] [INFO] GTDB search result was written to GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 13:27:11,886] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:27:11,890] [INFO] DFAST_QC result json was written to GCF_900100385.1_IMG-taxon_2651870124_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 13:27:11,890] [INFO] DFAST_QC completed!
[2024-01-24 13:27:11,890] [INFO] Total running time: 0h1m24s