[2024-01-25 20:07:05,481] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:07:05,482] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:07:05,482] [INFO] DQC Reference Directory: /var/lib/cwl/stg49fd19f7-bb30-4a9d-b752-44a73421de5c/dqc_reference
[2024-01-25 20:07:06,657] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:07:06,658] [INFO] Task started: Prodigal
[2024-01-25 20:07:06,658] [INFO] Running command: gunzip -c /var/lib/cwl/stg69531cac-ec63-4fbf-925b-e9982a5a6164/GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/cds.fna -a GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:07:19,796] [INFO] Task succeeded: Prodigal
[2024-01-25 20:07:19,797] [INFO] Task started: HMMsearch
[2024-01-25 20:07:19,797] [INFO] Running command: hmmsearch --tblout GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg49fd19f7-bb30-4a9d-b752-44a73421de5c/dqc_reference/reference_markers.hmm GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:07:20,027] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:07:20,028] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg69531cac-ec63-4fbf-925b-e9982a5a6164/GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna.gz]
[2024-01-25 20:07:20,055] [INFO] Query marker FASTA was written to GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:07:20,055] [INFO] Task started: Blastn
[2024-01-25 20:07:20,056] [INFO] Running command: blastn -query GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg49fd19f7-bb30-4a9d-b752-44a73421de5c/dqc_reference/reference_markers.fasta -out GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:07:20,570] [INFO] Task succeeded: Blastn
[2024-01-25 20:07:20,573] [INFO] Selected 8 target genomes.
[2024-01-25 20:07:20,573] [INFO] Target genome list was writen to GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:07:20,579] [INFO] Task started: fastANI
[2024-01-25 20:07:20,579] [INFO] Running command: fastANI --query /var/lib/cwl/stg69531cac-ec63-4fbf-925b-e9982a5a6164/GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna.gz --refList GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:07:27,579] [INFO] Task succeeded: fastANI
[2024-01-25 20:07:27,579] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg49fd19f7-bb30-4a9d-b752-44a73421de5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:07:27,579] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg49fd19f7-bb30-4a9d-b752-44a73421de5c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:07:27,586] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:07:27,586] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:07:27,586] [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
Natronoarchaeum philippinense	strain=DSM 27208	GCA_900215575.1	558529	558529	type	True	100.0	1050	1050	95	conclusive
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	86.024	830	1050	95	below_threshold
Halostella salina	strain=CBA1114	GCA_003675855.1	1547897	1547897	type	True	79.6888	519	1050	95	below_threshold
Halostella litorea	strain=DLLS-108	GCA_004785955.1	2528831	2528831	type	True	79.4695	514	1050	95	below_threshold
Halostella limicola	strain=LT12	GCA_003675875.1	2448456	2448456	type	True	78.9824	520	1050	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	78.789	426	1050	95	below_threshold
Halosimplex halophilum	strain=TH32	GCA_004698125.1	2559572	2559572	type	True	78.0401	456	1050	95	below_threshold
Halorussus rarus	strain=TBN4	GCA_003369835.1	660515	660515	type	True	78.0049	480	1050	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:07:27,588] [INFO] DFAST Taxonomy check result was written to GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:07:27,588] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:07:27,588] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:07:27,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg49fd19f7-bb30-4a9d-b752-44a73421de5c/dqc_reference/checkm_data
[2024-01-25 20:07:27,589] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:07:27,623] [INFO] Task started: CheckM
[2024-01-25 20:07:27,623] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/checkm_input GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:08:04,831] [INFO] Task succeeded: CheckM
[2024-01-25 20:08:04,832] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.45%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:08:04,857] [INFO] ===== Completeness check finished =====
[2024-01-25 20:08:04,857] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:08:04,858] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:08:04,859] [INFO] Task started: Blastn
[2024-01-25 20:08:04,859] [INFO] Running command: blastn -query GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg49fd19f7-bb30-4a9d-b752-44a73421de5c/dqc_reference/reference_markers_gtdb.fasta -out GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:08:05,454] [INFO] Task succeeded: Blastn
[2024-01-25 20:08:05,458] [INFO] Selected 11 target genomes.
[2024-01-25 20:08:05,458] [INFO] Target genome list was writen to GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:08:05,476] [INFO] Task started: fastANI
[2024-01-25 20:08:05,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg69531cac-ec63-4fbf-925b-e9982a5a6164/GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna.gz --refList GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:08:14,973] [INFO] Task succeeded: fastANI
[2024-01-25 20:08:14,980] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:08:14,981] [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_900215575.1	s__Natronoarchaeum philippinense	100.0	1050	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natronoarchaeaceae;g__Natronoarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003675855.1	s__Halostella salina	79.7498	513	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004785955.1	s__Halostella litorea	79.4716	512	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003675875.1	s__Halostella sp003675875	79.0005	518	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_003023565.1	s__Halostella sp003023565	78.805	428	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__QS-9-68-17;g__Halostella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112205.1	s__Halobiforma haloterrestris	78.7696	428	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	N/A	N/A	N/A	N/A	1	-
GCF_013415905.1	s__Halosimplex pelagicum	78.0895	444	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004698125.1	s__Halosimplex halophilum	78.04	457	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloarculaceae;g__Halosimplex	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003369835.1	s__Halorussus rarus	78.0247	478	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900111485.1	s__Natrinema hispanicum_A	77.8338	345	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	99.65	99.65	0.93	0.93	2	-
GCA_005239435.1	s__Halorussus sp005239435	77.7365	379	1050	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Halorussus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:08:14,982] [INFO] GTDB search result was written to GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:08:14,983] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:08:14,988] [INFO] DFAST_QC result json was written to GCF_900215575.1_IMG-taxon_2728369221_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:08:14,989] [INFO] DFAST_QC completed!
[2024-01-25 20:08:14,989] [INFO] Total running time: 0h1m10s