[2024-01-24 13:46:00,047] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:46:00,055] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:46:00,056] [INFO] DQC Reference Directory: /var/lib/cwl/stg9052c973-23f0-4427-81f6-f854f378501c/dqc_reference
[2024-01-24 13:46:01,426] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:46:01,427] [INFO] Task started: Prodigal
[2024-01-24 13:46:01,427] [INFO] Running command: gunzip -c /var/lib/cwl/stgf902f611-0052-49f7-8d7a-8d630f992a98/GCF_000191045.1_ASM19104v1_genomic.fna.gz | prodigal -d GCF_000191045.1_ASM19104v1_genomic.fna/cds.fna -a GCF_000191045.1_ASM19104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:04,156] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:04,156] [INFO] Task started: HMMsearch
[2024-01-24 13:46:04,156] [INFO] Running command: hmmsearch --tblout GCF_000191045.1_ASM19104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9052c973-23f0-4427-81f6-f854f378501c/dqc_reference/reference_markers.hmm GCF_000191045.1_ASM19104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:04,373] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:04,374] [INFO] Found 6/6 markers.
[2024-01-24 13:46:04,394] [INFO] Query marker FASTA was written to GCF_000191045.1_ASM19104v1_genomic.fna/markers.fasta
[2024-01-24 13:46:04,394] [INFO] Task started: Blastn
[2024-01-24 13:46:04,395] [INFO] Running command: blastn -query GCF_000191045.1_ASM19104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9052c973-23f0-4427-81f6-f854f378501c/dqc_reference/reference_markers.fasta -out GCF_000191045.1_ASM19104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:04,974] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:04,981] [INFO] Selected 17 target genomes.
[2024-01-24 13:46:04,981] [INFO] Target genome list was writen to GCF_000191045.1_ASM19104v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:05,184] [INFO] Task started: fastANI
[2024-01-24 13:46:05,184] [INFO] Running command: fastANI --query /var/lib/cwl/stgf902f611-0052-49f7-8d7a-8d630f992a98/GCF_000191045.1_ASM19104v1_genomic.fna.gz --refList GCF_000191045.1_ASM19104v1_genomic.fna/target_genomes.txt --output GCF_000191045.1_ASM19104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:12,886] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:12,886] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9052c973-23f0-4427-81f6-f854f378501c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:12,887] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9052c973-23f0-4427-81f6-f854f378501c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:12,897] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:12,897] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:12,898] [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
Desulfurobacterium thermolithotrophum	strain=DSM 11699	GCA_000191045.1	64160	64160	type	True	100.0	513	513	95	conclusive
Desulfurobacterium atlanticum	strain=DSM 15668	GCA_900188395.1	240169	240169	type	True	78.0154	60	513	95	below_threshold
Thermovibrio guaymasensis	strain=DSM 15521	GCA_003633715.1	240167	240167	type	True	77.8814	53	513	95	below_threshold
Phorcysia thermohydrogeniphila	strain=DSM 24425	GCA_004339575.1	936138	936138	type	True	77.4241	57	513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:12,899] [INFO] DFAST Taxonomy check result was written to GCF_000191045.1_ASM19104v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:12,900] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:12,900] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:12,900] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9052c973-23f0-4427-81f6-f854f378501c/dqc_reference/checkm_data
[2024-01-24 13:46:12,901] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:12,922] [INFO] Task started: CheckM
[2024-01-24 13:46:12,923] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000191045.1_ASM19104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000191045.1_ASM19104v1_genomic.fna/checkm_input GCF_000191045.1_ASM19104v1_genomic.fna/checkm_result
[2024-01-24 13:46:29,554] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:29,556] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:29,575] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:29,575] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:29,576] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000191045.1_ASM19104v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:29,576] [INFO] Task started: Blastn
[2024-01-24 13:46:29,576] [INFO] Running command: blastn -query GCF_000191045.1_ASM19104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9052c973-23f0-4427-81f6-f854f378501c/dqc_reference/reference_markers_gtdb.fasta -out GCF_000191045.1_ASM19104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:30,387] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:30,391] [INFO] Selected 18 target genomes.
[2024-01-24 13:46:30,391] [INFO] Target genome list was writen to GCF_000191045.1_ASM19104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:30,452] [INFO] Task started: fastANI
[2024-01-24 13:46:30,452] [INFO] Running command: fastANI --query /var/lib/cwl/stgf902f611-0052-49f7-8d7a-8d630f992a98/GCF_000191045.1_ASM19104v1_genomic.fna.gz --refList GCF_000191045.1_ASM19104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000191045.1_ASM19104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:37,112] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:37,123] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:37,123] [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_000191045.1	s__Desulfurobacterium thermolithotrophum	100.0	513	513	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium	95.0	95.79	95.79	0.88	0.88	2	conclusive
GCF_900188395.1	s__Desulfurobacterium_A atlanticum	78.0199	61	513	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Desulfurobacterium_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003633715.1	s__Thermovibrio guaymasensis	77.8814	53	513	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Thermovibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015488335.1	s__Balnearium sp015488335	77.5863	53	513	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Balnearium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004339575.1	s__Phorcysia thermohydrogeniphila	77.4241	57	513	d__Bacteria;p__Aquificota;c__Desulfurobacteriia;o__Desulfurobacteriales;f__Desulfurobacteriaceae;g__Phorcysia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:37,125] [INFO] GTDB search result was written to GCF_000191045.1_ASM19104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:37,126] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:37,129] [INFO] DFAST_QC result json was written to GCF_000191045.1_ASM19104v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:37,129] [INFO] DFAST_QC completed!
[2024-01-24 13:46:37,129] [INFO] Total running time: 0h0m37s