[2024-01-24 12:51:05,447] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:51:05,449] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:51:05,449] [INFO] DQC Reference Directory: /var/lib/cwl/stg84981dbd-1f01-4b12-b1a9-eba2bc3d8c02/dqc_reference
[2024-01-24 12:51:06,637] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:51:06,637] [INFO] Task started: Prodigal
[2024-01-24 12:51:06,637] [INFO] Running command: gunzip -c /var/lib/cwl/stgbd8748ab-50df-45ac-aadc-458133d20724/GCF_004339575.1_ASM433957v1_genomic.fna.gz | prodigal -d GCF_004339575.1_ASM433957v1_genomic.fna/cds.fna -a GCF_004339575.1_ASM433957v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:51:09,637] [INFO] Task succeeded: Prodigal
[2024-01-24 12:51:09,637] [INFO] Task started: HMMsearch
[2024-01-24 12:51:09,638] [INFO] Running command: hmmsearch --tblout GCF_004339575.1_ASM433957v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84981dbd-1f01-4b12-b1a9-eba2bc3d8c02/dqc_reference/reference_markers.hmm GCF_004339575.1_ASM433957v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:51:09,854] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:51:09,856] [INFO] Found 6/6 markers.
[2024-01-24 12:51:09,877] [INFO] Query marker FASTA was written to GCF_004339575.1_ASM433957v1_genomic.fna/markers.fasta
[2024-01-24 12:51:09,877] [INFO] Task started: Blastn
[2024-01-24 12:51:09,877] [INFO] Running command: blastn -query GCF_004339575.1_ASM433957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84981dbd-1f01-4b12-b1a9-eba2bc3d8c02/dqc_reference/reference_markers.fasta -out GCF_004339575.1_ASM433957v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:10,441] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:10,445] [INFO] Selected 14 target genomes.
[2024-01-24 12:51:10,445] [INFO] Target genome list was writen to GCF_004339575.1_ASM433957v1_genomic.fna/target_genomes.txt
[2024-01-24 12:51:10,464] [INFO] Task started: fastANI
[2024-01-24 12:51:10,464] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd8748ab-50df-45ac-aadc-458133d20724/GCF_004339575.1_ASM433957v1_genomic.fna.gz --refList GCF_004339575.1_ASM433957v1_genomic.fna/target_genomes.txt --output GCF_004339575.1_ASM433957v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:51:17,022] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:17,023] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84981dbd-1f01-4b12-b1a9-eba2bc3d8c02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:51:17,024] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84981dbd-1f01-4b12-b1a9-eba2bc3d8c02/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:51:17,034] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:51:17,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:51:17,035] [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
Phorcysia thermohydrogeniphila	strain=DSM 24425	GCA_004339575.1	936138	936138	type	True	100.0	536	537	95	conclusive
Thermovibrio guaymasensis	strain=DSM 15521	GCA_003633715.1	240167	240167	type	True	77.7617	134	537	95	below_threshold
Desulfurobacterium thermolithotrophum	strain=DSM 11699	GCA_000191045.1	64160	64160	type	True	77.4198	64	537	95	below_threshold
Balnearium lithotrophicum	strain=DSM 16304	GCA_900182585.1	223788	223788	type	True	77.2958	121	537	95	below_threshold
Thermovibrio ammonificans	strain=HB-1	GCA_000185805.1	228745	228745	type	True	77.1887	121	537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:51:17,036] [INFO] DFAST Taxonomy check result was written to GCF_004339575.1_ASM433957v1_genomic.fna/tc_result.tsv
[2024-01-24 12:51:17,037] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:51:17,037] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:51:17,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84981dbd-1f01-4b12-b1a9-eba2bc3d8c02/dqc_reference/checkm_data
[2024-01-24 12:51:17,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:51:17,056] [INFO] Task started: CheckM
[2024-01-24 12:51:17,057] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004339575.1_ASM433957v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004339575.1_ASM433957v1_genomic.fna/checkm_input GCF_004339575.1_ASM433957v1_genomic.fna/checkm_result
[2024-01-24 12:51:33,890] [INFO] Task succeeded: CheckM
[2024-01-24 12:51:33,892] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:51:33,910] [INFO] ===== Completeness check finished =====
[2024-01-24 12:51:33,910] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:51:33,911] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004339575.1_ASM433957v1_genomic.fna/markers.fasta)
[2024-01-24 12:51:33,911] [INFO] Task started: Blastn
[2024-01-24 12:51:33,911] [INFO] Running command: blastn -query GCF_004339575.1_ASM433957v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84981dbd-1f01-4b12-b1a9-eba2bc3d8c02/dqc_reference/reference_markers_gtdb.fasta -out GCF_004339575.1_ASM433957v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:51:34,692] [INFO] Task succeeded: Blastn
[2024-01-24 12:51:34,698] [INFO] Selected 18 target genomes.
[2024-01-24 12:51:34,699] [INFO] Target genome list was writen to GCF_004339575.1_ASM433957v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:51:34,716] [INFO] Task started: fastANI
[2024-01-24 12:51:34,717] [INFO] Running command: fastANI --query /var/lib/cwl/stgbd8748ab-50df-45ac-aadc-458133d20724/GCF_004339575.1_ASM433957v1_genomic.fna.gz --refList GCF_004339575.1_ASM433957v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004339575.1_ASM433957v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:51:41,687] [INFO] Task succeeded: fastANI
[2024-01-24 12:51:41,697] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:51:41,698] [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_004339575.1	s__Phorcysia thermohydrogeniphila	100.0	537	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Phorcysia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003978805.1	s__Phorcysia sp003978805	82.5792	206	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Phorcysia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488335.1	s__Balnearium sp015488335	77.9528	148	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Balnearium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015490195.1	s__Balnearium sp015490195	77.782	152	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Balnearium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633715.1	s__Thermovibrio guaymasensis	77.7559	135	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Thermovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000191045.1	s__Desulfurobacterium thermolithotrophum	77.4198	64	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium	95.0	95.79	95.79	0.88	0.88	2	-
GCF_900182585.1	s__Balnearium lithotrophicum	77.2719	122	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Balnearium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000185805.1	s__Thermovibrio ammonificans	77.1887	121	537	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Thermovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:51:41,699] [INFO] GTDB search result was written to GCF_004339575.1_ASM433957v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:51:41,700] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:51:41,702] [INFO] DFAST_QC result json was written to GCF_004339575.1_ASM433957v1_genomic.fna/dqc_result.json
[2024-01-24 12:51:41,703] [INFO] DFAST_QC completed!
[2024-01-24 12:51:41,703] [INFO] Total running time: 0h0m36s