[2024-01-25 20:12:50,672] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:50,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:50,674] [INFO] DQC Reference Directory: /var/lib/cwl/stg0323179c-d439-441a-8150-7061f5cb7872/dqc_reference
[2024-01-25 20:12:51,773] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:51,773] [INFO] Task started: Prodigal
[2024-01-25 20:12:51,773] [INFO] Running command: gunzip -c /var/lib/cwl/stgd740eece-457e-4e97-9863-8ec25df69808/GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/cds.fna -a GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:07,150] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:07,150] [INFO] Task started: HMMsearch
[2024-01-25 20:13:07,150] [INFO] Running command: hmmsearch --tblout GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0323179c-d439-441a-8150-7061f5cb7872/dqc_reference/reference_markers.hmm GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:07,397] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:07,398] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd740eece-457e-4e97-9863-8ec25df69808/GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna.gz]
[2024-01-25 20:13:07,430] [INFO] Query marker FASTA was written to GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:13:07,431] [INFO] Task started: Blastn
[2024-01-25 20:13:07,431] [INFO] Running command: blastn -query GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0323179c-d439-441a-8150-7061f5cb7872/dqc_reference/reference_markers.fasta -out GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:07,953] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:07,956] [INFO] Selected 10 target genomes.
[2024-01-25 20:13:07,956] [INFO] Target genome list was writen to GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:13:07,968] [INFO] Task started: fastANI
[2024-01-25 20:13:07,968] [INFO] Running command: fastANI --query /var/lib/cwl/stgd740eece-457e-4e97-9863-8ec25df69808/GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna.gz --refList GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:17,765] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:17,765] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0323179c-d439-441a-8150-7061f5cb7872/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:17,765] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0323179c-d439-441a-8150-7061f5cb7872/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:17,773] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:13:17,773] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:13:17,773] [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
Natronobacterium texcoconense	strain=DSM 24767	GCA_900104065.1	1095778	1095778	type	True	100.0	1332	1332	95	conclusive
Natronobacterium gregoryi	strain=SP2	GCA_002855455.1	44930	44930	type	True	85.2903	866	1332	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	85.2262	902	1332	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_000337655.1	44930	44930	type	True	85.1471	874	1332	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_000230715.3	44930	44930	type	True	85.1231	925	1332	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	83.1434	900	1332	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	83.1303	890	1332	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	81.4464	760	1332	95	below_threshold
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	81.4258	768	1332	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	81.4036	796	1332	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:17,775] [INFO] DFAST Taxonomy check result was written to GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:13:17,776] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:17,776] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:17,776] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0323179c-d439-441a-8150-7061f5cb7872/dqc_reference/checkm_data
[2024-01-25 20:13:17,777] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:17,816] [INFO] Task started: CheckM
[2024-01-25 20:13:17,816] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/checkm_input GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:14:00,436] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:00,437] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:00,485] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:00,485] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:00,486] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:14:00,486] [INFO] Task started: Blastn
[2024-01-25 20:14:00,486] [INFO] Running command: blastn -query GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg0323179c-d439-441a-8150-7061f5cb7872/dqc_reference/reference_markers_gtdb.fasta -out GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:01,044] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:01,047] [INFO] Selected 9 target genomes.
[2024-01-25 20:14:01,047] [INFO] Target genome list was writen to GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:01,054] [INFO] Task started: fastANI
[2024-01-25 20:14:01,054] [INFO] Running command: fastANI --query /var/lib/cwl/stgd740eece-457e-4e97-9863-8ec25df69808/GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna.gz --refList GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:11,165] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:11,171] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:14:11,171] [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_900104065.1	s__Natronobacterium texcoconense	100.0	1332	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000230715.2	s__Natronobacterium gregoryi	85.1461	923	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	99.99	99.97	1.00	1.00	4	-
GCF_900112205.1	s__Halobiforma haloterrestris	83.1434	901	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	83.1433	889	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_000337895.1	s__Halobiforma nitratireducens	82.5422	750	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000217715.1	s__Halopiger xanaduensis	81.4987	754	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000455345.1	s__Halopiger_A goleimassiliensis	81.4389	765	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	81.4303	792	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352155.1	s__Haloterrigena sp017352155	81.313	686	1332	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:11,173] [INFO] GTDB search result was written to GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:11,174] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:11,176] [INFO] DFAST_QC result json was written to GCF_900104065.1_IMG-taxon_2636416047_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:14:11,176] [INFO] DFAST_QC completed!
[2024-01-25 20:14:11,176] [INFO] Total running time: 0h1m21s