[2024-01-25 20:13:50,574] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:13:50,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:13:50,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg1dfdd958-a83a-4db0-ab3c-47334e9736c2/dqc_reference
[2024-01-25 20:13:51,872] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:13:51,873] [INFO] Task started: Prodigal
[2024-01-25 20:13:51,873] [INFO] Running command: gunzip -c /var/lib/cwl/stge6cd97fd-9d4f-42b6-857f-47825dd81299/GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/cds.fna -a GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:13:54,039] [INFO] Task succeeded: Prodigal
[2024-01-25 20:13:54,039] [INFO] Task started: HMMsearch
[2024-01-25 20:13:54,039] [INFO] Running command: hmmsearch --tblout GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1dfdd958-a83a-4db0-ab3c-47334e9736c2/dqc_reference/reference_markers.hmm GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:13:54,282] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:13:54,283] [INFO] Found 6/6 markers.
[2024-01-25 20:13:54,303] [INFO] Query marker FASTA was written to GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:13:54,303] [INFO] Task started: Blastn
[2024-01-25 20:13:54,303] [INFO] Running command: blastn -query GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dfdd958-a83a-4db0-ab3c-47334e9736c2/dqc_reference/reference_markers.fasta -out GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:13:54,861] [INFO] Task succeeded: Blastn
[2024-01-25 20:13:54,865] [INFO] Selected 12 target genomes.
[2024-01-25 20:13:54,865] [INFO] Target genome list was writen to GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:13:54,874] [INFO] Task started: fastANI
[2024-01-25 20:13:54,875] [INFO] Running command: fastANI --query /var/lib/cwl/stge6cd97fd-9d4f-42b6-857f-47825dd81299/GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna.gz --refList GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:13:58,724] [INFO] Task succeeded: fastANI
[2024-01-25 20:13:58,725] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1dfdd958-a83a-4db0-ab3c-47334e9736c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:13:58,725] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1dfdd958-a83a-4db0-ab3c-47334e9736c2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:13:58,729] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 20:13:58,729] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 20:13:58,729] [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
Hydrogenothermus marinus	strain=VM1	GCA_003688665.1	133270	133270	type	True	77.1765	170	499	95	below_threshold
Sulfurihydrogenibium yellowstonense	strain=SS-5	GCA_000173615.1	304736	304736	type	True	76.9679	100	499	95	below_threshold
Persephonella atlantica	strain=MO1340	GCA_016617615.1	2699429	2699429	type	True	76.5753	51	499	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:13:58,731] [INFO] DFAST Taxonomy check result was written to GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:13:58,731] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:13:58,731] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:13:58,731] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1dfdd958-a83a-4db0-ab3c-47334e9736c2/dqc_reference/checkm_data
[2024-01-25 20:13:58,732] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:13:58,752] [INFO] Task started: CheckM
[2024-01-25 20:13:58,752] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/checkm_input GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:14:12,952] [INFO] Task succeeded: CheckM
[2024-01-25 20:14:12,953] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:14:12,970] [INFO] ===== Completeness check finished =====
[2024-01-25 20:14:12,971] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:14:12,971] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:14:12,971] [INFO] Task started: Blastn
[2024-01-25 20:14:12,971] [INFO] Running command: blastn -query GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stg1dfdd958-a83a-4db0-ab3c-47334e9736c2/dqc_reference/reference_markers_gtdb.fasta -out GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:14:13,704] [INFO] Task succeeded: Blastn
[2024-01-25 20:14:13,706] [INFO] Selected 16 target genomes.
[2024-01-25 20:14:13,707] [INFO] Target genome list was writen to GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:14:13,718] [INFO] Task started: fastANI
[2024-01-25 20:14:13,718] [INFO] Running command: fastANI --query /var/lib/cwl/stge6cd97fd-9d4f-42b6-857f-47825dd81299/GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna.gz --refList GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:14:18,777] [INFO] Task succeeded: fastANI
[2024-01-25 20:14:18,785] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 20:14:18,785] [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_000020325.1	s__Sulfurihydrogenibium sp000020325	77.4035	133	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Sulfurihydrogenibium	95.0	99.85	99.85	0.98	0.98	2	-
GCF_003688665.1	s__Hydrogenothermus marinus	77.1932	169	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015519975.1	s__Hydrogenothermus sp015519975	76.8803	123	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490675.1	s__Hydrogenothermus sp015490675	76.6952	107	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_012961365.1	s__Hydrogenothermus sp012961365	76.5998	96	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	99.54	99.54	0.76	0.76	2	-
GCF_016617615.1	s__Persephonella atlantica	76.5753	51	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003978675.1	s__Hydrogenothermus sp003978675	76.4803	110	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Hydrogenothermus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013153795.1	s__JAADDV01 sp013153795	76.389	109	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__JAADDV01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015487465.1	s__Persephonella sp015487465	75.9606	58	499	d__Bacteria;p__Aquificota;c__Aquificae;o__Hydrogenothermales;f__Hydrogenothermaceae;g__Persephonella	95.0	99.63	99.63	0.92	0.92	2	-
GCF_004365575.1	s__Hypnocyclicus thermotrophus	74.5903	50	499	d__Bacteria;p__Fusobacteriota;c__Fusobacteriia;o__Fusobacteriales;f__Fusobacteriaceae;g__Hypnocyclicus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:14:18,787] [INFO] GTDB search result was written to GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:14:18,788] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:14:18,791] [INFO] DFAST_QC result json was written to GCF_900182795.1_IMG-taxon_2724679818_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:14:18,791] [INFO] DFAST_QC completed!
[2024-01-25 20:14:18,791] [INFO] Total running time: 0h0m28s