[2024-01-25 18:56:05,550] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:56:05,551] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:56:05,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg2d45babe-363f-4e0a-9adc-9cf2cd599bc4/dqc_reference
[2024-01-25 18:56:06,674] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:56:06,674] [INFO] Task started: Prodigal
[2024-01-25 18:56:06,675] [INFO] Running command: gunzip -c /var/lib/cwl/stg8caa23c4-3905-481f-963f-153bb4cb3358/GCF_009392895.1_ASM939289v1_genomic.fna.gz | prodigal -d GCF_009392895.1_ASM939289v1_genomic.fna/cds.fna -a GCF_009392895.1_ASM939289v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:56:25,146] [INFO] Task succeeded: Prodigal
[2024-01-25 18:56:25,146] [INFO] Task started: HMMsearch
[2024-01-25 18:56:25,146] [INFO] Running command: hmmsearch --tblout GCF_009392895.1_ASM939289v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2d45babe-363f-4e0a-9adc-9cf2cd599bc4/dqc_reference/reference_markers.hmm GCF_009392895.1_ASM939289v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:56:25,396] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:56:25,397] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg8caa23c4-3905-481f-963f-153bb4cb3358/GCF_009392895.1_ASM939289v1_genomic.fna.gz]
[2024-01-25 18:56:25,431] [INFO] Query marker FASTA was written to GCF_009392895.1_ASM939289v1_genomic.fna/markers.fasta
[2024-01-25 18:56:25,431] [INFO] Task started: Blastn
[2024-01-25 18:56:25,431] [INFO] Running command: blastn -query GCF_009392895.1_ASM939289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d45babe-363f-4e0a-9adc-9cf2cd599bc4/dqc_reference/reference_markers.fasta -out GCF_009392895.1_ASM939289v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:25,928] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:25,930] [INFO] Selected 7 target genomes.
[2024-01-25 18:56:25,930] [INFO] Target genome list was writen to GCF_009392895.1_ASM939289v1_genomic.fna/target_genomes.txt
[2024-01-25 18:56:25,934] [INFO] Task started: fastANI
[2024-01-25 18:56:25,934] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caa23c4-3905-481f-963f-153bb4cb3358/GCF_009392895.1_ASM939289v1_genomic.fna.gz --refList GCF_009392895.1_ASM939289v1_genomic.fna/target_genomes.txt --output GCF_009392895.1_ASM939289v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:56:33,561] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:33,561] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2d45babe-363f-4e0a-9adc-9cf2cd599bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:56:33,562] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2d45babe-363f-4e0a-9adc-9cf2cd599bc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:56:33,568] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:56:33,568] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:56:33,568] [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
Natronorubrum aibiense	strain=7-3	GCA_009392895.1	348826	348826	type	True	100.0	1447	1447	95	conclusive
Natronorubrum sulfidifaciens	strain=JCM 14089	GCA_000337735.1	388259	388259	type	True	88.2576	912	1447	95	below_threshold
Natronorubrum bangense	strain=JCM 10635	GCA_004799645.1	61858	61858	type	True	85.4586	961	1447	95	below_threshold
Natronorubrum bangense	strain=JCM 10635	GCA_000337715.1	61858	61858	type	True	85.3519	946	1447	95	below_threshold
Haloterrigena turkmenica	strain=DSM 5511	GCA_000025325.1	62320	62320	type	True	81.7577	827	1447	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	81.7385	805	1447	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	81.6542	806	1447	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:56:33,569] [INFO] DFAST Taxonomy check result was written to GCF_009392895.1_ASM939289v1_genomic.fna/tc_result.tsv
[2024-01-25 18:56:33,569] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:56:33,570] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:56:33,570] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2d45babe-363f-4e0a-9adc-9cf2cd599bc4/dqc_reference/checkm_data
[2024-01-25 18:56:33,571] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:56:33,614] [INFO] Task started: CheckM
[2024-01-25 18:56:33,614] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009392895.1_ASM939289v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009392895.1_ASM939289v1_genomic.fna/checkm_input GCF_009392895.1_ASM939289v1_genomic.fna/checkm_result
[2024-01-25 18:57:24,201] [INFO] Task succeeded: CheckM
[2024-01-25 18:57:24,203] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:57:24,224] [INFO] ===== Completeness check finished =====
[2024-01-25 18:57:24,224] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:57:24,225] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009392895.1_ASM939289v1_genomic.fna/markers.fasta)
[2024-01-25 18:57:24,225] [INFO] Task started: Blastn
[2024-01-25 18:57:24,226] [INFO] Running command: blastn -query GCF_009392895.1_ASM939289v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2d45babe-363f-4e0a-9adc-9cf2cd599bc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_009392895.1_ASM939289v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:57:24,741] [INFO] Task succeeded: Blastn
[2024-01-25 18:57:24,744] [INFO] Selected 7 target genomes.
[2024-01-25 18:57:24,744] [INFO] Target genome list was writen to GCF_009392895.1_ASM939289v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:57:24,751] [INFO] Task started: fastANI
[2024-01-25 18:57:24,751] [INFO] Running command: fastANI --query /var/lib/cwl/stg8caa23c4-3905-481f-963f-153bb4cb3358/GCF_009392895.1_ASM939289v1_genomic.fna.gz --refList GCF_009392895.1_ASM939289v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009392895.1_ASM939289v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:57:33,117] [INFO] Task succeeded: fastANI
[2024-01-25 18:57:33,123] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:57:33,124] [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_009392895.1	s__Natronorubrum aibiense	100.0	1447	1447	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000337735.1	s__Natronorubrum sulfidifaciens	88.2617	912	1447	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156475.1	s__Natronorubrum thiooxidans	87.4559	1042	1447	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004799645.1	s__Natronorubrum bangense	85.4651	960	1447	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	97.90	95.84	0.96	0.96	3	-
GCF_900100335.1	s__Natronorubrum texcoconense	82.0335	844	1447	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	81.6805	803	1447	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337215.1	s__Natronolimnohabitans innermongolicus	81.4812	780	1447	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:57:33,126] [INFO] GTDB search result was written to GCF_009392895.1_ASM939289v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:57:33,126] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:57:33,129] [INFO] DFAST_QC result json was written to GCF_009392895.1_ASM939289v1_genomic.fna/dqc_result.json
[2024-01-25 18:57:33,129] [INFO] DFAST_QC completed!
[2024-01-25 18:57:33,129] [INFO] Total running time: 0h1m28s