[2024-01-24 13:42:57,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,166] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,167] [INFO] DQC Reference Directory: /var/lib/cwl/stgab61546d-5da3-4097-9991-e90f13914a21/dqc_reference
[2024-01-24 13:42:58,405] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,405] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,406] [INFO] Running command: gunzip -c /var/lib/cwl/stg719c53c9-b75d-4f1f-a176-b892f0de8f02/GCF_000159095.1_ASM15909v1_genomic.fna.gz | prodigal -d GCF_000159095.1_ASM15909v1_genomic.fna/cds.fna -a GCF_000159095.1_ASM15909v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:02,190] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:02,190] [INFO] Task started: HMMsearch
[2024-01-24 13:43:02,191] [INFO] Running command: hmmsearch --tblout GCF_000159095.1_ASM15909v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgab61546d-5da3-4097-9991-e90f13914a21/dqc_reference/reference_markers.hmm GCF_000159095.1_ASM15909v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:02,427] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:02,429] [INFO] Found 6/6 markers.
[2024-01-24 13:43:02,452] [INFO] Query marker FASTA was written to GCF_000159095.1_ASM15909v1_genomic.fna/markers.fasta
[2024-01-24 13:43:02,452] [INFO] Task started: Blastn
[2024-01-24 13:43:02,453] [INFO] Running command: blastn -query GCF_000159095.1_ASM15909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab61546d-5da3-4097-9991-e90f13914a21/dqc_reference/reference_markers.fasta -out GCF_000159095.1_ASM15909v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:03,033] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:03,037] [INFO] Selected 8 target genomes.
[2024-01-24 13:43:03,037] [INFO] Target genome list was writen to GCF_000159095.1_ASM15909v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:03,077] [INFO] Task started: fastANI
[2024-01-24 13:43:03,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg719c53c9-b75d-4f1f-a176-b892f0de8f02/GCF_000159095.1_ASM15909v1_genomic.fna.gz --refList GCF_000159095.1_ASM15909v1_genomic.fna/target_genomes.txt --output GCF_000159095.1_ASM15909v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:07,260] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:07,261] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgab61546d-5da3-4097-9991-e90f13914a21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:07,261] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgab61546d-5da3-4097-9991-e90f13914a21/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:07,272] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:07,272] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:07,273] [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 tetradius	strain=ATCC 35098	GCA_000159095.1	33036	33036	type	True	99.9998	684	690	95	conclusive
Anaerococcus prevotii	strain=NCTC11806	GCA_900445285.1	33034	33034	type	True	81.621	359	690	95	below_threshold
Anaerococcus prevotii	strain=DSM 20548	GCA_000024105.1	33034	33034	type	True	81.5739	358	690	95	below_threshold
Anaerococcus vaginimassiliensis	strain=Marseille-P4512	GCA_900626155.1	2042308	2042308	type	True	81.5323	286	690	95	below_threshold
Anaerococcus marasmi	strain=Marseille-P3557	GCA_900290195.1	2057797	2057797	type	True	81.3312	350	690	95	below_threshold
Anaerococcus lactolyticus	strain=ATCC 51172	GCA_000156575.1	33032	33032	type	True	81.2118	200	690	95	below_threshold
Anaerococcus mediterraneensis	strain=Marseille-P2765	GCA_900128415.1	1870984	1870984	type	True	80.3527	178	690	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:07,274] [INFO] DFAST Taxonomy check result was written to GCF_000159095.1_ASM15909v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:07,275] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:07,275] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:07,275] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgab61546d-5da3-4097-9991-e90f13914a21/dqc_reference/checkm_data
[2024-01-24 13:43:07,276] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:07,301] [INFO] Task started: CheckM
[2024-01-24 13:43:07,302] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000159095.1_ASM15909v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000159095.1_ASM15909v1_genomic.fna/checkm_input GCF_000159095.1_ASM15909v1_genomic.fna/checkm_result
[2024-01-24 13:43:25,872] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:25,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:25,901] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:25,901] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:25,902] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000159095.1_ASM15909v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:25,902] [INFO] Task started: Blastn
[2024-01-24 13:43:25,902] [INFO] Running command: blastn -query GCF_000159095.1_ASM15909v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgab61546d-5da3-4097-9991-e90f13914a21/dqc_reference/reference_markers_gtdb.fasta -out GCF_000159095.1_ASM15909v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:26,688] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:26,692] [INFO] Selected 11 target genomes.
[2024-01-24 13:43:26,692] [INFO] Target genome list was writen to GCF_000159095.1_ASM15909v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:26,703] [INFO] Task started: fastANI
[2024-01-24 13:43:26,703] [INFO] Running command: fastANI --query /var/lib/cwl/stg719c53c9-b75d-4f1f-a176-b892f0de8f02/GCF_000159095.1_ASM15909v1_genomic.fna.gz --refList GCF_000159095.1_ASM15909v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000159095.1_ASM15909v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:31,212] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:31,224] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:31,225] [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_000159095.1	s__Anaerococcus tetradius	99.9998	684	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.20	98.20	0.90	0.90	2	conclusive
GCF_900258475.1	s__Anaerococcus sp900258475	82.3098	221	690	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_000024105.1	s__Anaerococcus prevotii	81.5703	359	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900626155.1	s__Anaerococcus vaginimassiliensis	81.4974	290	690	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_900290195.1	s__Anaerococcus marasmi	81.3302	350	690	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_017874475.1	s__Anaerococcus degeneri	81.1066	172	690	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_000156575.1	s__Anaerococcus lactolyticus	81.0923	202	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	97.67	97.67	0.89	0.89	2	-
GCF_900128415.1	s__Anaerococcus mediterraneensis	80.3735	178	690	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_000312365.2	s__Anaerococcus provencensis	80.0235	166	690	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_017874535.1	s__Anaerococcus nagyae	77.7942	124	690	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.14	98.91	0.93	0.91	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:31,226] [INFO] GTDB search result was written to GCF_000159095.1_ASM15909v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:31,227] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:31,230] [INFO] DFAST_QC result json was written to GCF_000159095.1_ASM15909v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:31,230] [INFO] DFAST_QC completed!
[2024-01-24 13:43:31,230] [INFO] Total running time: 0h0m34s