[2024-01-24 11:59:12,706] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:59:12,712] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:59:12,713] [INFO] DQC Reference Directory: /var/lib/cwl/stg693aaabc-a631-41e5-84b0-07f4ad2cb1e7/dqc_reference
[2024-01-24 11:59:14,027] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:59:14,028] [INFO] Task started: Prodigal
[2024-01-24 11:59:14,028] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a361394-3afb-46b6-8a80-80b1a62f2622/GCF_016617615.1_ASM1661761v1_genomic.fna.gz | prodigal -d GCF_016617615.1_ASM1661761v1_genomic.fna/cds.fna -a GCF_016617615.1_ASM1661761v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:17,710] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:17,711] [INFO] Task started: HMMsearch
[2024-01-24 11:59:17,711] [INFO] Running command: hmmsearch --tblout GCF_016617615.1_ASM1661761v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg693aaabc-a631-41e5-84b0-07f4ad2cb1e7/dqc_reference/reference_markers.hmm GCF_016617615.1_ASM1661761v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:17,994] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:17,995] [INFO] Found 6/6 markers.
[2024-01-24 11:59:18,019] [INFO] Query marker FASTA was written to GCF_016617615.1_ASM1661761v1_genomic.fna/markers.fasta
[2024-01-24 11:59:18,020] [INFO] Task started: Blastn
[2024-01-24 11:59:18,020] [INFO] Running command: blastn -query GCF_016617615.1_ASM1661761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg693aaabc-a631-41e5-84b0-07f4ad2cb1e7/dqc_reference/reference_markers.fasta -out GCF_016617615.1_ASM1661761v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:18,673] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:18,676] [INFO] Selected 12 target genomes.
[2024-01-24 11:59:18,677] [INFO] Target genome list was writen to GCF_016617615.1_ASM1661761v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:18,684] [INFO] Task started: fastANI
[2024-01-24 11:59:18,685] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a361394-3afb-46b6-8a80-80b1a62f2622/GCF_016617615.1_ASM1661761v1_genomic.fna.gz --refList GCF_016617615.1_ASM1661761v1_genomic.fna/target_genomes.txt --output GCF_016617615.1_ASM1661761v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:24,714] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:24,714] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg693aaabc-a631-41e5-84b0-07f4ad2cb1e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:24,715] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg693aaabc-a631-41e5-84b0-07f4ad2cb1e7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:24,721] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:59:24,722] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:24,722] [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
Persephonella atlantica	strain=MO1340	GCA_016617615.1	2699429	2699429	type	True	100.0	629	630	95	conclusive
Persephonella hydrogeniphila	strain=DSM 15103	GCA_900215515.1	198703	198703	type	True	78.0489	284	630	95	below_threshold
Persephonella marina	strain=EX-H1	GCA_000021565.1	309805	309805	type	True	77.6602	174	630	95	below_threshold
Hydrogenothermus marinus	strain=VM1	GCA_003688665.1	133270	133270	type	True	76.5126	85	630	95	below_threshold
Sulfurihydrogenibium azorense	strain=Az-Fu1	GCA_000021545.1	309806	309806	type	True	76.409	53	630	95	below_threshold
Sulfurihydrogenibium subterraneum	strain=DSM 15120	GCA_000619805.1	171121	171121	type	True	76.103	60	630	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:59:24,724] [INFO] DFAST Taxonomy check result was written to GCF_016617615.1_ASM1661761v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:24,725] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:24,725] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:24,725] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg693aaabc-a631-41e5-84b0-07f4ad2cb1e7/dqc_reference/checkm_data
[2024-01-24 11:59:24,726] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:24,747] [INFO] Task started: CheckM
[2024-01-24 11:59:24,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016617615.1_ASM1661761v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016617615.1_ASM1661761v1_genomic.fna/checkm_input GCF_016617615.1_ASM1661761v1_genomic.fna/checkm_result
[2024-01-24 11:59:44,630] [INFO] Task succeeded: CheckM
[2024-01-24 11:59:44,631] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:59:44,651] [INFO] ===== Completeness check finished =====
[2024-01-24 11:59:44,651] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:59:44,652] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016617615.1_ASM1661761v1_genomic.fna/markers.fasta)
[2024-01-24 11:59:44,652] [INFO] Task started: Blastn
[2024-01-24 11:59:44,653] [INFO] Running command: blastn -query GCF_016617615.1_ASM1661761v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg693aaabc-a631-41e5-84b0-07f4ad2cb1e7/dqc_reference/reference_markers_gtdb.fasta -out GCF_016617615.1_ASM1661761v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:45,461] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:45,465] [INFO] Selected 11 target genomes.
[2024-01-24 11:59:45,466] [INFO] Target genome list was writen to GCF_016617615.1_ASM1661761v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:59:45,475] [INFO] Task started: fastANI
[2024-01-24 11:59:45,476] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a361394-3afb-46b6-8a80-80b1a62f2622/GCF_016617615.1_ASM1661761v1_genomic.fna.gz --refList GCF_016617615.1_ASM1661761v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016617615.1_ASM1661761v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:59:49,476] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:49,485] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:59:49,485] [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_016617615.1	s__Persephonella atlantica	100.0	629	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015487465.1	s__Persephonella sp015487465	78.1515	273	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	99.63	99.63	0.92	0.92	2	-
GCF_000703085.1	s__Persephonella sp000703085	77.9802	239	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000703045.1	s__Persephonella sp000703045	77.9353	217	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021565.1	s__Persephonella marina	77.6602	174	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_013153235.1	s__Persephonella sp013153235	77.3858	165	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153795.1	s__JAADDV01 sp013153795	77.0475	109	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__JAADDV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015519975.1	s__Hydrogenothermus sp015519975	76.8575	81	630	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:59:49,487] [INFO] GTDB search result was written to GCF_016617615.1_ASM1661761v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:59:49,488] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:59:49,492] [INFO] DFAST_QC result json was written to GCF_016617615.1_ASM1661761v1_genomic.fna/dqc_result.json
[2024-01-24 11:59:49,492] [INFO] DFAST_QC completed!
[2024-01-24 11:59:49,492] [INFO] Total running time: 0h0m37s