[2024-01-24 14:05:33,794] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:33,797] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:33,797] [INFO] DQC Reference Directory: /var/lib/cwl/stg39d57049-f8ea-4d0b-966b-7d4afdc89059/dqc_reference
[2024-01-24 14:05:35,116] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:35,117] [INFO] Task started: Prodigal
[2024-01-24 14:05:35,118] [INFO] Running command: gunzip -c /var/lib/cwl/stg084bd852-1eb8-47ea-acaa-7c5038bf6730/GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/cds.fna -a GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:59,192] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:59,192] [INFO] Task started: HMMsearch
[2024-01-24 14:05:59,192] [INFO] Running command: hmmsearch --tblout GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg39d57049-f8ea-4d0b-966b-7d4afdc89059/dqc_reference/reference_markers.hmm GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:59,448] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:59,449] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg084bd852-1eb8-47ea-acaa-7c5038bf6730/GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna.gz]
[2024-01-24 14:05:59,489] [INFO] Query marker FASTA was written to GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 14:05:59,490] [INFO] Task started: Blastn
[2024-01-24 14:05:59,490] [INFO] Running command: blastn -query GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg39d57049-f8ea-4d0b-966b-7d4afdc89059/dqc_reference/reference_markers.fasta -out GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:00,025] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:00,033] [INFO] Selected 7 target genomes.
[2024-01-24 14:06:00,033] [INFO] Target genome list was writen to GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 14:06:00,047] [INFO] Task started: fastANI
[2024-01-24 14:06:00,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg084bd852-1eb8-47ea-acaa-7c5038bf6730/GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna.gz --refList GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:07,551] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:07,552] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg39d57049-f8ea-4d0b-966b-7d4afdc89059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:07,552] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg39d57049-f8ea-4d0b-966b-7d4afdc89059/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:07,559] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:06:07,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:07,560] [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
Haladaptatus paucihalophilus	strain=DX253	GCA_900142335.1	367189	367189	type	True	100.0	1422	1422	95	conclusive
Haladaptatus paucihalophilus	strain=DX253	GCA_000187225.2	367189	367189	type	True	99.9977	1401	1422	95	conclusive
Haladaptatus paucihalophilus	strain=DX253	GCA_000376445.1	367189	367189	type	True	99.9929	1418	1422	95	conclusive
Haladaptatus pallidirubidus	strain=YIM 93656	GCA_020700235.1	1008152	1008152	type	True	81.0352	779	1422	95	below_threshold
Haladaptatus litoreus	strain=CGMCC 1.7737	GCA_900156425.1	553468	553468	type	True	80.9989	808	1422	95	below_threshold
Haladaptatus cibarius	strain=D43	GCA_000710615.1	453847	453847	type	True	80.9206	783	1422	95	below_threshold
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	76.9516	323	1422	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:07,561] [INFO] DFAST Taxonomy check result was written to GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 14:06:07,562] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:07,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:07,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg39d57049-f8ea-4d0b-966b-7d4afdc89059/dqc_reference/checkm_data
[2024-01-24 14:06:07,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:07,608] [INFO] Task started: CheckM
[2024-01-24 14:06:07,608] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/checkm_input GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 14:07:09,067] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:09,068] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:09,086] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:09,086] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:09,087] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 14:07:09,087] [INFO] Task started: Blastn
[2024-01-24 14:07:09,087] [INFO] Running command: blastn -query GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg39d57049-f8ea-4d0b-966b-7d4afdc89059/dqc_reference/reference_markers_gtdb.fasta -out GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:09,572] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:09,575] [INFO] Selected 8 target genomes.
[2024-01-24 14:07:09,575] [INFO] Target genome list was writen to GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:09,581] [INFO] Task started: fastANI
[2024-01-24 14:07:09,581] [INFO] Running command: fastANI --query /var/lib/cwl/stg084bd852-1eb8-47ea-acaa-7c5038bf6730/GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna.gz --refList GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:17,550] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:17,559] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:17,559] [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_000376445.1	s__Haladaptatus paucihalophilus	99.9929	1418	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	98.84	96.52	0.92	0.76	4	conclusive
GCF_001625445.1	s__Haladaptatus sp001625445	84.6412	1035	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156425.1	s__Haladaptatus litoreus	80.986	810	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000710615.1	s__Haladaptatus cibarius	80.9339	780	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003298465.1	s__Haladaptatus sp003298465	79.2887	664	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	78.1173	490	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900113245.1	s__Halopelagius inordinatus	77.548	362	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halopelagius	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009176545.1	s__Salinigranum salinum	76.9164	310	1422	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Salinigranum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:17,561] [INFO] GTDB search result was written to GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:17,562] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:17,569] [INFO] DFAST_QC result json was written to GCF_900142335.1_IMG-taxon_2698536698_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 14:07:17,569] [INFO] DFAST_QC completed!
[2024-01-24 14:07:17,570] [INFO] Total running time: 0h1m44s