[2024-01-24 13:18:26,433] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:26,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:26,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg524cfa68-75b3-4f10-9b30-8bd76e5717b0/dqc_reference
[2024-01-24 13:18:27,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:27,591] [INFO] Task started: Prodigal
[2024-01-24 13:18:27,591] [INFO] Running command: gunzip -c /var/lib/cwl/stg065e23dc-5620-436c-8b1f-0686855a378d/GCF_000021545.1_ASM2154v1_genomic.fna.gz | prodigal -d GCF_000021545.1_ASM2154v1_genomic.fna/cds.fna -a GCF_000021545.1_ASM2154v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:30,231] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:30,232] [INFO] Task started: HMMsearch
[2024-01-24 13:18:30,232] [INFO] Running command: hmmsearch --tblout GCF_000021545.1_ASM2154v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg524cfa68-75b3-4f10-9b30-8bd76e5717b0/dqc_reference/reference_markers.hmm GCF_000021545.1_ASM2154v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:30,415] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:30,416] [INFO] Found 6/6 markers.
[2024-01-24 13:18:30,434] [INFO] Query marker FASTA was written to GCF_000021545.1_ASM2154v1_genomic.fna/markers.fasta
[2024-01-24 13:18:30,434] [INFO] Task started: Blastn
[2024-01-24 13:18:30,435] [INFO] Running command: blastn -query GCF_000021545.1_ASM2154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524cfa68-75b3-4f10-9b30-8bd76e5717b0/dqc_reference/reference_markers.fasta -out GCF_000021545.1_ASM2154v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:30,987] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:30,990] [INFO] Selected 10 target genomes.
[2024-01-24 13:18:30,991] [INFO] Target genome list was writen to GCF_000021545.1_ASM2154v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:31,000] [INFO] Task started: fastANI
[2024-01-24 13:18:31,000] [INFO] Running command: fastANI --query /var/lib/cwl/stg065e23dc-5620-436c-8b1f-0686855a378d/GCF_000021545.1_ASM2154v1_genomic.fna.gz --refList GCF_000021545.1_ASM2154v1_genomic.fna/target_genomes.txt --output GCF_000021545.1_ASM2154v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:34,985] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:34,985] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg524cfa68-75b3-4f10-9b30-8bd76e5717b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:34,986] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg524cfa68-75b3-4f10-9b30-8bd76e5717b0/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:34,993] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:34,993] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:34,993] [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
Sulfurihydrogenibium azorense	strain=Az-Fu1	GCA_000021545.1	309806	309806	type	True	100.0	546	546	95	conclusive
Sulfurihydrogenibium subterraneum	strain=DSM 15120	GCA_000619805.1	171121	171121	type	True	87.575	461	546	95	below_threshold
Sulfurihydrogenibium yellowstonense	strain=SS-5	GCA_000173615.1	304736	304736	type	True	77.7343	132	546	95	below_threshold
Persephonella marina	strain=EX-H1	GCA_000021565.1	309805	309805	type	True	76.5392	61	546	95	below_threshold
Hydrogenothermus marinus	strain=VM1	GCA_003688665.1	133270	133270	type	True	76.2242	95	546	95	below_threshold
Persephonella hydrogeniphila	strain=DSM 15103	GCA_900215515.1	198703	198703	type	True	76.1728	75	546	95	below_threshold
Persephonella atlantica	strain=MO1340	GCA_016617615.1	2699429	2699429	type	True	76.1012	62	546	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:34,995] [INFO] DFAST Taxonomy check result was written to GCF_000021545.1_ASM2154v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:34,995] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:34,996] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:34,996] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg524cfa68-75b3-4f10-9b30-8bd76e5717b0/dqc_reference/checkm_data
[2024-01-24 13:18:34,997] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:35,014] [INFO] Task started: CheckM
[2024-01-24 13:18:35,015] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000021545.1_ASM2154v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000021545.1_ASM2154v1_genomic.fna/checkm_input GCF_000021545.1_ASM2154v1_genomic.fna/checkm_result
[2024-01-24 13:18:50,896] [INFO] Task succeeded: CheckM
[2024-01-24 13:18:50,897] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:18:50,950] [INFO] ===== Completeness check finished =====
[2024-01-24 13:18:50,950] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:18:50,951] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000021545.1_ASM2154v1_genomic.fna/markers.fasta)
[2024-01-24 13:18:50,951] [INFO] Task started: Blastn
[2024-01-24 13:18:50,951] [INFO] Running command: blastn -query GCF_000021545.1_ASM2154v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg524cfa68-75b3-4f10-9b30-8bd76e5717b0/dqc_reference/reference_markers_gtdb.fasta -out GCF_000021545.1_ASM2154v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:51,766] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:51,770] [INFO] Selected 11 target genomes.
[2024-01-24 13:18:51,770] [INFO] Target genome list was writen to GCF_000021545.1_ASM2154v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:18:51,811] [INFO] Task started: fastANI
[2024-01-24 13:18:51,812] [INFO] Running command: fastANI --query /var/lib/cwl/stg065e23dc-5620-436c-8b1f-0686855a378d/GCF_000021545.1_ASM2154v1_genomic.fna.gz --refList GCF_000021545.1_ASM2154v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000021545.1_ASM2154v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:18:55,792] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,800] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:18:55,801] [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_000021545.1	s__Sulfurihydrogenibium azorense	100.0	546	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000619805.1	s__Sulfurihydrogenibium subterraneum	87.5445	462	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002878035.1	s__Sulfurihydrogenibium sp002878035	79.2761	236	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	98.45	98.45	0.81	0.81	2	-
GCF_000173615.1	s__Sulfurihydrogenibium yellowstonense	77.7103	133	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000020325.1	s__Sulfurihydrogenibium sp000020325	77.5109	196	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	99.85	99.85	0.98	0.98	2	-
GCA_015519975.1	s__Hydrogenothermus sp015519975	76.3102	77	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000021565.1	s__Persephonella marina	76.2909	59	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016617615.1	s__Persephonella atlantica	76.1012	62	546	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,803] [INFO] GTDB search result was written to GCF_000021545.1_ASM2154v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:18:55,804] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:18:55,807] [INFO] DFAST_QC result json was written to GCF_000021545.1_ASM2154v1_genomic.fna/dqc_result.json
[2024-01-24 13:18:55,807] [INFO] DFAST_QC completed!
[2024-01-24 13:18:55,808] [INFO] Total running time: 0h0m29s