[2024-01-24 14:31:14,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,773] [INFO] DQC Reference Directory: /var/lib/cwl/stg546de3ea-6b62-41b0-acb3-e07f34977c75/dqc_reference
[2024-01-24 14:31:16,042] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,043] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,044] [INFO] Running command: gunzip -c /var/lib/cwl/stgeefde4b4-b754-4092-a84b-068867b89a2a/GCF_016726485.1_ASM1672648v1_genomic.fna.gz | prodigal -d GCF_016726485.1_ASM1672648v1_genomic.fna/cds.fna -a GCF_016726485.1_ASM1672648v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:19,898] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:19,899] [INFO] Task started: HMMsearch
[2024-01-24 14:31:19,899] [INFO] Running command: hmmsearch --tblout GCF_016726485.1_ASM1672648v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg546de3ea-6b62-41b0-acb3-e07f34977c75/dqc_reference/reference_markers.hmm GCF_016726485.1_ASM1672648v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:20,167] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:20,169] [INFO] Found 6/6 markers.
[2024-01-24 14:31:20,189] [INFO] Query marker FASTA was written to GCF_016726485.1_ASM1672648v1_genomic.fna/markers.fasta
[2024-01-24 14:31:20,190] [INFO] Task started: Blastn
[2024-01-24 14:31:20,190] [INFO] Running command: blastn -query GCF_016726485.1_ASM1672648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg546de3ea-6b62-41b0-acb3-e07f34977c75/dqc_reference/reference_markers.fasta -out GCF_016726485.1_ASM1672648v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:20,830] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:20,841] [INFO] Selected 7 target genomes.
[2024-01-24 14:31:20,841] [INFO] Target genome list was writen to GCF_016726485.1_ASM1672648v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:20,844] [INFO] Task started: fastANI
[2024-01-24 14:31:20,844] [INFO] Running command: fastANI --query /var/lib/cwl/stgeefde4b4-b754-4092-a84b-068867b89a2a/GCF_016726485.1_ASM1672648v1_genomic.fna.gz --refList GCF_016726485.1_ASM1672648v1_genomic.fna/target_genomes.txt --output GCF_016726485.1_ASM1672648v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:31:24,169] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:24,169] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg546de3ea-6b62-41b0-acb3-e07f34977c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:31:24,169] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg546de3ea-6b62-41b0-acb3-e07f34977c75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:31:24,177] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:31:24,178] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:31:24,178] [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
Peptoniphilus harei	strain=FDAARGOS_1136	GCA_016726485.1	54005	54005	suspected-type	True	100.0	641	643	95	conclusive
Peptoniphilus harei	strain=NCTC13076	GCA_900454685.1	54005	54005	suspected-type	True	99.999	632	643	95	conclusive
Peptoniphilus vaginalis	strain=KhD- 2	GCA_900176605.1	1756987	1756987	type	True	87.45	453	643	95	below_threshold
Peptoniphilus phoceensis	strain=SIT15	GCA_001517665.2	1720298	1720298	type	True	85.1168	463	643	95	below_threshold
Peptoniphilus timonensis	strain=JC401	GCA_000312025.1	1268254	1268254	type	True	84.6786	448	643	95	below_threshold
Peptoniphilus obesi	strain=ph1	GCA_000311865.1	1472765	1472765	type	True	83.8267	114	643	95	below_threshold
Peptoniphilus gorbachii	strain=DSM 21461	GCA_016908115.1	411567	411567	type	True	83.5955	416	643	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:31:24,179] [INFO] DFAST Taxonomy check result was written to GCF_016726485.1_ASM1672648v1_genomic.fna/tc_result.tsv
[2024-01-24 14:31:24,180] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:31:24,180] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:31:24,180] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg546de3ea-6b62-41b0-acb3-e07f34977c75/dqc_reference/checkm_data
[2024-01-24 14:31:24,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:31:24,211] [INFO] Task started: CheckM
[2024-01-24 14:31:24,211] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_016726485.1_ASM1672648v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_016726485.1_ASM1672648v1_genomic.fna/checkm_input GCF_016726485.1_ASM1672648v1_genomic.fna/checkm_result
[2024-01-24 14:31:44,193] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:44,194] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:44,211] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:44,212] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:44,212] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_016726485.1_ASM1672648v1_genomic.fna/markers.fasta)
[2024-01-24 14:31:44,212] [INFO] Task started: Blastn
[2024-01-24 14:31:44,213] [INFO] Running command: blastn -query GCF_016726485.1_ASM1672648v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg546de3ea-6b62-41b0-acb3-e07f34977c75/dqc_reference/reference_markers_gtdb.fasta -out GCF_016726485.1_ASM1672648v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:45,119] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:45,123] [INFO] Selected 7 target genomes.
[2024-01-24 14:31:45,123] [INFO] Target genome list was writen to GCF_016726485.1_ASM1672648v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:45,130] [INFO] Task started: fastANI
[2024-01-24 14:31:45,130] [INFO] Running command: fastANI --query /var/lib/cwl/stgeefde4b4-b754-4092-a84b-068867b89a2a/GCF_016726485.1_ASM1672648v1_genomic.fna.gz --refList GCF_016726485.1_ASM1672648v1_genomic.fna/target_genomes_gtdb.txt --output GCF_016726485.1_ASM1672648v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:48,754] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:48,768] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:48,769] [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_900454685.1	s__Peptoniphilus_A harei	99.999	631	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.43	96.58	0.91	0.87	7	conclusive
GCF_000183565.1	s__Peptoniphilus_A harei_A	88.938	505	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	96.93	96.82	0.90	0.88	5	-
GCF_900176605.1	s__Peptoniphilus_A vaginalis	87.45	453	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	97.24	97.24	0.91	0.91	2	-
GCF_001517665.2	s__Peptoniphilus_A phoceensis	85.0992	465	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	100.00	100.00	1.00	1.00	2	-
GCF_000312025.1	s__Peptoniphilus_A timonensis	84.6786	448	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	96.7724	N/A	N/A	N/A	N/A	1	-
GCF_000311865.1	s__Peptoniphilus_E obesi	83.8267	114	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_E	95.0	100.00	100.00	1.00	1.00	2	-
GCF_016908115.1	s__Peptoniphilus_A gorbachii	83.6119	415	643	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Peptoniphilus_A	95.0	96.70	96.17	0.85	0.82	5	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:48,770] [INFO] GTDB search result was written to GCF_016726485.1_ASM1672648v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:48,771] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:48,774] [INFO] DFAST_QC result json was written to GCF_016726485.1_ASM1672648v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:48,774] [INFO] DFAST_QC completed!
[2024-01-24 14:31:48,774] [INFO] Total running time: 0h0m34s