[2024-01-24 13:40:28,888] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:28,890] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:28,891] [INFO] DQC Reference Directory: /var/lib/cwl/stg3c8ca22c-cbc7-41eb-930b-cec38bb22e9a/dqc_reference
[2024-01-24 13:40:30,325] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:30,326] [INFO] Task started: Prodigal
[2024-01-24 13:40:30,326] [INFO] Running command: gunzip -c /var/lib/cwl/stgf23df744-4fea-4ec2-95b9-778f8bcf426d/GCF_008245085.1_ASM824508v1_genomic.fna.gz | prodigal -d GCF_008245085.1_ASM824508v1_genomic.fna/cds.fna -a GCF_008245085.1_ASM824508v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:40:34,498] [INFO] Task succeeded: Prodigal
[2024-01-24 13:40:34,498] [INFO] Task started: HMMsearch
[2024-01-24 13:40:34,498] [INFO] Running command: hmmsearch --tblout GCF_008245085.1_ASM824508v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3c8ca22c-cbc7-41eb-930b-cec38bb22e9a/dqc_reference/reference_markers.hmm GCF_008245085.1_ASM824508v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:40:34,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:40:34,677] [WARNING] Found 2/6 markers. [/var/lib/cwl/stgf23df744-4fea-4ec2-95b9-778f8bcf426d/GCF_008245085.1_ASM824508v1_genomic.fna.gz]
[2024-01-24 13:40:34,699] [INFO] Query marker FASTA was written to GCF_008245085.1_ASM824508v1_genomic.fna/markers.fasta
[2024-01-24 13:40:34,700] [INFO] Task started: Blastn
[2024-01-24 13:40:34,700] [INFO] Running command: blastn -query GCF_008245085.1_ASM824508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c8ca22c-cbc7-41eb-930b-cec38bb22e9a/dqc_reference/reference_markers.fasta -out GCF_008245085.1_ASM824508v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:35,193] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:35,197] [INFO] Selected 4 target genomes.
[2024-01-24 13:40:35,197] [INFO] Target genome list was writen to GCF_008245085.1_ASM824508v1_genomic.fna/target_genomes.txt
[2024-01-24 13:40:35,203] [INFO] Task started: fastANI
[2024-01-24 13:40:35,203] [INFO] Running command: fastANI --query /var/lib/cwl/stgf23df744-4fea-4ec2-95b9-778f8bcf426d/GCF_008245085.1_ASM824508v1_genomic.fna.gz --refList GCF_008245085.1_ASM824508v1_genomic.fna/target_genomes.txt --output GCF_008245085.1_ASM824508v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:40:37,058] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:37,059] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3c8ca22c-cbc7-41eb-930b-cec38bb22e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:40:37,059] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3c8ca22c-cbc7-41eb-930b-cec38bb22e9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:40:37,065] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:40:37,066] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:40:37,066] [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
Pyrococcus furiosus	strain=DSM 3638	GCA_008245085.1	2261	2261	type	True	100.0	629	629	95	conclusive
Pyrococcus furiosus	strain=DSM 3638	GCA_000007305.1	2261	2261	type	True	99.9751	627	629	95	conclusive
Pyrococcus horikoshii	strain=OT3	GCA_000011105.1	53953	53953	type	True	79.5812	148	629	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:40:37,073] [INFO] DFAST Taxonomy check result was written to GCF_008245085.1_ASM824508v1_genomic.fna/tc_result.tsv
[2024-01-24 13:40:37,073] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:40:37,074] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:40:37,074] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3c8ca22c-cbc7-41eb-930b-cec38bb22e9a/dqc_reference/checkm_data
[2024-01-24 13:40:37,075] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:40:37,097] [INFO] Task started: CheckM
[2024-01-24 13:40:37,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008245085.1_ASM824508v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008245085.1_ASM824508v1_genomic.fna/checkm_input GCF_008245085.1_ASM824508v1_genomic.fna/checkm_result
[2024-01-24 13:40:56,707] [INFO] Task succeeded: CheckM
[2024-01-24 13:40:56,708] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:40:56,725] [INFO] ===== Completeness check finished =====
[2024-01-24 13:40:56,725] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:40:56,725] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008245085.1_ASM824508v1_genomic.fna/markers.fasta)
[2024-01-24 13:40:56,726] [INFO] Task started: Blastn
[2024-01-24 13:40:56,726] [INFO] Running command: blastn -query GCF_008245085.1_ASM824508v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3c8ca22c-cbc7-41eb-930b-cec38bb22e9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_008245085.1_ASM824508v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:40:57,228] [INFO] Task succeeded: Blastn
[2024-01-24 13:40:57,232] [INFO] Selected 3 target genomes.
[2024-01-24 13:40:57,232] [INFO] Target genome list was writen to GCF_008245085.1_ASM824508v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:40:57,235] [INFO] Task started: fastANI
[2024-01-24 13:40:57,235] [INFO] Running command: fastANI --query /var/lib/cwl/stgf23df744-4fea-4ec2-95b9-778f8bcf426d/GCF_008245085.1_ASM824508v1_genomic.fna.gz --refList GCF_008245085.1_ASM824508v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008245085.1_ASM824508v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:40:58,584] [INFO] Task succeeded: fastANI
[2024-01-24 13:40:58,588] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:40:58,588] [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_000007305.1	s__Pyrococcus furiosus	99.9751	627	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Pyrococcus	95.0	99.95	99.93	1.00	1.00	3	conclusive
GCF_000011105.1	s__Pyrococcus horikoshii	79.6345	146	629	d__Archaea;p__Methanobacteriota_B;c__Thermococci;o__Thermococcales;f__Thermococcaceae;g__Pyrococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:40:58,590] [INFO] GTDB search result was written to GCF_008245085.1_ASM824508v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:40:58,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:40:58,593] [INFO] DFAST_QC result json was written to GCF_008245085.1_ASM824508v1_genomic.fna/dqc_result.json
[2024-01-24 13:40:58,593] [INFO] DFAST_QC completed!
[2024-01-24 13:40:58,593] [INFO] Total running time: 0h0m30s