[2024-01-24 10:57:38,788] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:57:38,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:57:38,794] [INFO] DQC Reference Directory: /var/lib/cwl/stgca34b00f-8c03-4418-89ea-fc9edf1572ea/dqc_reference
[2024-01-24 10:57:40,194] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:57:40,195] [INFO] Task started: Prodigal
[2024-01-24 10:57:40,196] [INFO] Running command: gunzip -c /var/lib/cwl/stgcf2be1bf-d5e5-4343-b2f8-bbd02592ec44/GCF_900445285.1_49888_A01_genomic.fna.gz | prodigal -d GCF_900445285.1_49888_A01_genomic.fna/cds.fna -a GCF_900445285.1_49888_A01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:57:43,811] [INFO] Task succeeded: Prodigal
[2024-01-24 10:57:43,812] [INFO] Task started: HMMsearch
[2024-01-24 10:57:43,812] [INFO] Running command: hmmsearch --tblout GCF_900445285.1_49888_A01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgca34b00f-8c03-4418-89ea-fc9edf1572ea/dqc_reference/reference_markers.hmm GCF_900445285.1_49888_A01_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:57:44,023] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:57:44,024] [INFO] Found 6/6 markers.
[2024-01-24 10:57:44,047] [INFO] Query marker FASTA was written to GCF_900445285.1_49888_A01_genomic.fna/markers.fasta
[2024-01-24 10:57:44,048] [INFO] Task started: Blastn
[2024-01-24 10:57:44,048] [INFO] Running command: blastn -query GCF_900445285.1_49888_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgca34b00f-8c03-4418-89ea-fc9edf1572ea/dqc_reference/reference_markers.fasta -out GCF_900445285.1_49888_A01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:57:44,631] [INFO] Task succeeded: Blastn
[2024-01-24 10:57:44,634] [INFO] Selected 6 target genomes.
[2024-01-24 10:57:44,635] [INFO] Target genome list was writen to GCF_900445285.1_49888_A01_genomic.fna/target_genomes.txt
[2024-01-24 10:57:44,685] [INFO] Task started: fastANI
[2024-01-24 10:57:44,685] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2be1bf-d5e5-4343-b2f8-bbd02592ec44/GCF_900445285.1_49888_A01_genomic.fna.gz --refList GCF_900445285.1_49888_A01_genomic.fna/target_genomes.txt --output GCF_900445285.1_49888_A01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:57:48,103] [INFO] Task succeeded: fastANI
[2024-01-24 10:57:48,104] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgca34b00f-8c03-4418-89ea-fc9edf1572ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:57:48,105] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgca34b00f-8c03-4418-89ea-fc9edf1572ea/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:57:48,147] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:57:48,148] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:57:48,148] [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
Anaerococcus prevotii	strain=NCTC11806	GCA_900445285.1	33034	33034	type	True	100.0	667	668	95	conclusive
Anaerococcus prevotii	strain=DSM 20548	GCA_000024105.1	33034	33034	type	True	99.9918	666	668	95	conclusive
Anaerococcus marasmi	strain=Marseille-P3557	GCA_900290195.1	2057797	2057797	type	True	92.4128	548	668	95	below_threshold
Anaerococcus vaginimassiliensis	strain=Marseille-P4512	GCA_900626155.1	2042308	2042308	type	True	82.1953	313	668	95	below_threshold
Anaerococcus tetradius	strain=ATCC 35098	GCA_000159095.1	33036	33036	type	True	81.7229	353	668	95	below_threshold
Anaerococcus octavius	strain=NCTC9810	GCA_900445265.1	54007	54007	type	True	80.5829	121	668	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:57:48,149] [INFO] DFAST Taxonomy check result was written to GCF_900445285.1_49888_A01_genomic.fna/tc_result.tsv
[2024-01-24 10:57:48,150] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:57:48,150] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:57:48,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgca34b00f-8c03-4418-89ea-fc9edf1572ea/dqc_reference/checkm_data
[2024-01-24 10:57:48,155] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:57:48,177] [INFO] Task started: CheckM
[2024-01-24 10:57:48,178] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900445285.1_49888_A01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900445285.1_49888_A01_genomic.fna/checkm_input GCF_900445285.1_49888_A01_genomic.fna/checkm_result
[2024-01-24 10:58:09,138] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:09,139] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:09,166] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:09,166] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:09,167] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900445285.1_49888_A01_genomic.fna/markers.fasta)
[2024-01-24 10:58:09,168] [INFO] Task started: Blastn
[2024-01-24 10:58:09,168] [INFO] Running command: blastn -query GCF_900445285.1_49888_A01_genomic.fna/markers.fasta -db /var/lib/cwl/stgca34b00f-8c03-4418-89ea-fc9edf1572ea/dqc_reference/reference_markers_gtdb.fasta -out GCF_900445285.1_49888_A01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:10,453] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:10,457] [INFO] Selected 8 target genomes.
[2024-01-24 10:58:10,457] [INFO] Target genome list was writen to GCF_900445285.1_49888_A01_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:10,464] [INFO] Task started: fastANI
[2024-01-24 10:58:10,465] [INFO] Running command: fastANI --query /var/lib/cwl/stgcf2be1bf-d5e5-4343-b2f8-bbd02592ec44/GCF_900445285.1_49888_A01_genomic.fna.gz --refList GCF_900445285.1_49888_A01_genomic.fna/target_genomes_gtdb.txt --output GCF_900445285.1_49888_A01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:14,441] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:14,466] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:14,466] [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_000024105.1	s__Anaerococcus prevotii	99.9918	665	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900290195.1	s__Anaerococcus marasmi	92.481	545	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900626155.1	s__Anaerococcus vaginimassiliensis	82.1945	310	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	95.85	95.85	0.94	0.94	2	-
GCF_000159095.1	s__Anaerococcus tetradius	81.7271	352	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.20	98.20	0.90	0.90	2	-
GCF_000312365.2	s__Anaerococcus provencensis	81.0081	162	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900128415.1	s__Anaerococcus mediterraneensis	80.8935	160	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900258475.1	s__Anaerococcus sp900258475	80.6766	223	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	96.55	96.55	0.87	0.87	2	-
GCF_900445265.1	s__Anaerococcus octavius	80.5883	121	668	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.32	98.32	0.89	0.88	3	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:14,468] [INFO] GTDB search result was written to GCF_900445285.1_49888_A01_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:14,468] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:14,472] [INFO] DFAST_QC result json was written to GCF_900445285.1_49888_A01_genomic.fna/dqc_result.json
[2024-01-24 10:58:14,472] [INFO] DFAST_QC completed!
[2024-01-24 10:58:14,473] [INFO] Total running time: 0h0m36s