[2024-01-24 13:25:29,053] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:29,058] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:29,059] [INFO] DQC Reference Directory: /var/lib/cwl/stg5b06e6b8-cec2-4d81-9159-2de25a84f56e/dqc_reference
[2024-01-24 13:25:30,411] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:30,411] [INFO] Task started: Prodigal
[2024-01-24 13:25:30,412] [INFO] Running command: gunzip -c /var/lib/cwl/stgd534506a-6d01-43fb-a81b-caf0968982db/GCF_000011205.1_ASM1120v1_genomic.fna.gz | prodigal -d GCF_000011205.1_ASM1120v1_genomic.fna/cds.fna -a GCF_000011205.1_ASM1120v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:37,600] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:37,600] [INFO] Task started: HMMsearch
[2024-01-24 13:25:37,600] [INFO] Running command: hmmsearch --tblout GCF_000011205.1_ASM1120v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5b06e6b8-cec2-4d81-9159-2de25a84f56e/dqc_reference/reference_markers.hmm GCF_000011205.1_ASM1120v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:37,837] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:37,838] [WARNING] Found 1/6 markers. [/var/lib/cwl/stgd534506a-6d01-43fb-a81b-caf0968982db/GCF_000011205.1_ASM1120v1_genomic.fna.gz]
[2024-01-24 13:25:37,868] [INFO] Query marker FASTA was written to GCF_000011205.1_ASM1120v1_genomic.fna/markers.fasta
[2024-01-24 13:25:37,868] [INFO] Task started: Blastn
[2024-01-24 13:25:37,868] [INFO] Running command: blastn -query GCF_000011205.1_ASM1120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b06e6b8-cec2-4d81-9159-2de25a84f56e/dqc_reference/reference_markers.fasta -out GCF_000011205.1_ASM1120v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:38,407] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:38,411] [INFO] Selected 3 target genomes.
[2024-01-24 13:25:38,411] [INFO] Target genome list was writen to GCF_000011205.1_ASM1120v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:38,448] [INFO] Task started: fastANI
[2024-01-24 13:25:38,448] [INFO] Running command: fastANI --query /var/lib/cwl/stgd534506a-6d01-43fb-a81b-caf0968982db/GCF_000011205.1_ASM1120v1_genomic.fna.gz --refList GCF_000011205.1_ASM1120v1_genomic.fna/target_genomes.txt --output GCF_000011205.1_ASM1120v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:41,237] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:41,238] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5b06e6b8-cec2-4d81-9159-2de25a84f56e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:41,239] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5b06e6b8-cec2-4d81-9159-2de25a84f56e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:41,246] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:25:41,246] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:25:41,247] [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
Sulfurisphaera tokodaii	strain=7	GCA_000011205.1	111955	111955	type	True	100.0	898	898	95	inconclusive
Sulfurisphaera ohwakuensis	strain=DSM 12421	GCA_014202105.1	69656	69656	type	True	95.0144	750	898	95	inconclusive
Sulfurisphaera ohwakuensis	strain=TA-1	GCA_009729055.1	69656	69656	type	True	94.9561	766	898	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:41,249] [INFO] DFAST Taxonomy check result was written to GCF_000011205.1_ASM1120v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:41,249] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:41,249] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:41,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5b06e6b8-cec2-4d81-9159-2de25a84f56e/dqc_reference/checkm_data
[2024-01-24 13:25:41,251] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:41,286] [INFO] Task started: CheckM
[2024-01-24 13:25:41,287] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000011205.1_ASM1120v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000011205.1_ASM1120v1_genomic.fna/checkm_input GCF_000011205.1_ASM1120v1_genomic.fna/checkm_result
[2024-01-24 13:26:08,045] [INFO] Task succeeded: CheckM
[2024-01-24 13:26:08,047] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 83.33%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:26:08,084] [INFO] ===== Completeness check finished =====
[2024-01-24 13:26:08,084] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:26:08,084] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000011205.1_ASM1120v1_genomic.fna/markers.fasta)
[2024-01-24 13:26:08,085] [INFO] Task started: Blastn
[2024-01-24 13:26:08,085] [INFO] Running command: blastn -query GCF_000011205.1_ASM1120v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5b06e6b8-cec2-4d81-9159-2de25a84f56e/dqc_reference/reference_markers_gtdb.fasta -out GCF_000011205.1_ASM1120v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:26:08,554] [INFO] Task succeeded: Blastn
[2024-01-24 13:26:08,557] [INFO] Selected 3 target genomes.
[2024-01-24 13:26:08,557] [INFO] Target genome list was writen to GCF_000011205.1_ASM1120v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:26:08,560] [INFO] Task started: fastANI
[2024-01-24 13:26:08,560] [INFO] Running command: fastANI --query /var/lib/cwl/stgd534506a-6d01-43fb-a81b-caf0968982db/GCF_000011205.1_ASM1120v1_genomic.fna.gz --refList GCF_000011205.1_ASM1120v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000011205.1_ASM1120v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:26:11,286] [INFO] Task succeeded: fastANI
[2024-01-24 13:26:11,290] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:26:11,290] [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_000011205.1	s__Sulfurisphaera tokodaii	100.0	898	898	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_009729055.1	s__Sulfurisphaera ohwakuensis	94.9173	768	898	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	100.00	100.00	1.00	1.00	2	-
GCF_012222305.1	s__Sulfurisphaera sp012222305	90.3566	724	898	d__Archaea;p__Thermoproteota;c__Thermoproteia;o__Sulfolobales;f__Sulfolobaceae;g__Sulfurisphaera	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:26:11,292] [INFO] GTDB search result was written to GCF_000011205.1_ASM1120v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:26:11,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:26:11,294] [INFO] DFAST_QC result json was written to GCF_000011205.1_ASM1120v1_genomic.fna/dqc_result.json
[2024-01-24 13:26:11,294] [INFO] DFAST_QC completed!
[2024-01-24 13:26:11,294] [INFO] Total running time: 0h0m42s