[2024-01-24 13:40:28,416] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,419] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,419] [INFO] DQC Reference Directory: /var/lib/cwl/stg24ba9955-02c9-4312-beba-92c123cf8af1/dqc_reference
[2024-01-24 13:40:29,961] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:29,962] [INFO] Task started: Prodigal
[2024-01-24 13:40:29,963] [INFO] Running command: gunzip -c /var/lib/cwl/stgf58f4444-8f86-40ca-81b8-8db0f814e3bc/GCF_020405205.1_ASM2040520v1_genomic.fna.gz | prodigal -d GCF_020405205.1_ASM2040520v1_genomic.fna/cds.fna -a GCF_020405205.1_ASM2040520v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:52,845] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:52,845] [INFO] Task started: HMMsearch
[2024-01-24 13:40:52,846] [INFO] Running command: hmmsearch --tblout GCF_020405205.1_ASM2040520v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24ba9955-02c9-4312-beba-92c123cf8af1/dqc_reference/reference_markers.hmm GCF_020405205.1_ASM2040520v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:53,153] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:53,154] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgf58f4444-8f86-40ca-81b8-8db0f814e3bc/GCF_020405205.1_ASM2040520v1_genomic.fna.gz]
[2024-01-24 13:40:53,198] [INFO] Query marker FASTA was written to GCF_020405205.1_ASM2040520v1_genomic.fna/markers.fasta
[2024-01-24 13:40:53,198] [INFO] Task started: Blastn
[2024-01-24 13:40:53,198] [INFO] Running command: blastn -query GCF_020405205.1_ASM2040520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24ba9955-02c9-4312-beba-92c123cf8af1/dqc_reference/reference_markers.fasta -out GCF_020405205.1_ASM2040520v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:53,773] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:53,776] [INFO] Selected 8 target genomes.
[2024-01-24 13:40:53,776] [INFO] Target genome list was writen to GCF_020405205.1_ASM2040520v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:53,784] [INFO] Task started: fastANI
[2024-01-24 13:40:53,784] [INFO] Running command: fastANI --query /var/lib/cwl/stgf58f4444-8f86-40ca-81b8-8db0f814e3bc/GCF_020405205.1_ASM2040520v1_genomic.fna.gz --refList GCF_020405205.1_ASM2040520v1_genomic.fna/target_genomes.txt --output GCF_020405205.1_ASM2040520v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:01,974] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:01,975] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24ba9955-02c9-4312-beba-92c123cf8af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:01,975] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24ba9955-02c9-4312-beba-92c123cf8af1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:01,983] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:41:01,984] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:41:01,984] [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
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	85.8646	1069	1566	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	85.4196	1037	1566	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	84.8633	948	1566	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	84.617	897	1566	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	84.5566	889	1566	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	84.2738	855	1566	95	below_threshold
Natrinema gari	strain=JCM 14663	GCA_000337175.1	419186	419186	type	True	84.1964	867	1566	95	below_threshold
Haloterrigena limicola	strain=JCM 13563	GCA_000337475.1	370323	370323	type	True	82.4134	736	1566	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:01,985] [INFO] DFAST Taxonomy check result was written to GCF_020405205.1_ASM2040520v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:01,986] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:01,986] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:01,986] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24ba9955-02c9-4312-beba-92c123cf8af1/dqc_reference/checkm_data
[2024-01-24 13:41:01,987] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:02,034] [INFO] Task started: CheckM
[2024-01-24 13:41:02,035] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_020405205.1_ASM2040520v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_020405205.1_ASM2040520v1_genomic.fna/checkm_input GCF_020405205.1_ASM2040520v1_genomic.fna/checkm_result
[2024-01-24 13:42:00,341] [INFO] Task succeeded: CheckM
[2024-01-24 13:42:00,342] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:42:00,362] [INFO] ===== Completeness check finished =====
[2024-01-24 13:42:00,363] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:42:00,363] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_020405205.1_ASM2040520v1_genomic.fna/markers.fasta)
[2024-01-24 13:42:00,363] [INFO] Task started: Blastn
[2024-01-24 13:42:00,364] [INFO] Running command: blastn -query GCF_020405205.1_ASM2040520v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24ba9955-02c9-4312-beba-92c123cf8af1/dqc_reference/reference_markers_gtdb.fasta -out GCF_020405205.1_ASM2040520v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:42:00,921] [INFO] Task succeeded: Blastn
[2024-01-24 13:42:00,924] [INFO] Selected 9 target genomes.
[2024-01-24 13:42:00,924] [INFO] Target genome list was writen to GCF_020405205.1_ASM2040520v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:42:00,930] [INFO] Task started: fastANI
[2024-01-24 13:42:00,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgf58f4444-8f86-40ca-81b8-8db0f814e3bc/GCF_020405205.1_ASM2040520v1_genomic.fna.gz --refList GCF_020405205.1_ASM2040520v1_genomic.fna/target_genomes_gtdb.txt --output GCF_020405205.1_ASM2040520v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:42:10,654] [INFO] Task succeeded: fastANI
[2024-01-24 13:42:10,663] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:42:10,663] [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_002494345.1	s__Natrinema ejinorense	85.4604	969	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_900110865.1	s__Natrinema salaciae	85.4084	1039	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005576615.1	s__Natrinema versiforme_A	85.0741	984	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337195.1	s__Natrinema versiforme	84.8306	952	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731985.1	s__Natrinema altunense	84.6084	898	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	-
GCF_013456555.1	s__Natrinema sp013456555	84.542	913	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002572525.1	s__Natrinema sp002572525	84.4013	1007	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337615.1	s__Natrinema pallidum	84.2794	854	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
GCF_000337175.1	s__Natrinema gari	84.1899	868	1566	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.50	98.45	0.93	0.92	3	-
--------------------------------------------------------------------------------
[2024-01-24 13:42:10,665] [INFO] GTDB search result was written to GCF_020405205.1_ASM2040520v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:42:10,666] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:42:10,669] [INFO] DFAST_QC result json was written to GCF_020405205.1_ASM2040520v1_genomic.fna/dqc_result.json
[2024-01-24 13:42:10,669] [INFO] DFAST_QC completed!
[2024-01-24 13:42:10,669] [INFO] Total running time: 0h1m42s