[2024-01-24 12:53:41,582] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:53:41,584] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:53:41,584] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ab84521-3f55-492b-9cf5-17ebecff3c0b/dqc_reference
[2024-01-24 12:53:42,996] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:53:42,998] [INFO] Task started: Prodigal
[2024-01-24 12:53:42,999] [INFO] Running command: gunzip -c /var/lib/cwl/stgf786a989-e8ab-4771-8853-bd21666907eb/GCF_000173355.1_ASM17335v1_genomic.fna.gz | prodigal -d GCF_000173355.1_ASM17335v1_genomic.fna/cds.fna -a GCF_000173355.1_ASM17335v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:53:46,324] [INFO] Task succeeded: Prodigal
[2024-01-24 12:53:46,324] [INFO] Task started: HMMsearch
[2024-01-24 12:53:46,325] [INFO] Running command: hmmsearch --tblout GCF_000173355.1_ASM17335v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ab84521-3f55-492b-9cf5-17ebecff3c0b/dqc_reference/reference_markers.hmm GCF_000173355.1_ASM17335v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:53:46,648] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:53:46,649] [INFO] Found 6/6 markers.
[2024-01-24 12:53:46,683] [INFO] Query marker FASTA was written to GCF_000173355.1_ASM17335v1_genomic.fna/markers.fasta
[2024-01-24 12:53:46,683] [INFO] Task started: Blastn
[2024-01-24 12:53:46,684] [INFO] Running command: blastn -query GCF_000173355.1_ASM17335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab84521-3f55-492b-9cf5-17ebecff3c0b/dqc_reference/reference_markers.fasta -out GCF_000173355.1_ASM17335v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:47,967] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:47,970] [INFO] Selected 6 target genomes.
[2024-01-24 12:53:47,970] [INFO] Target genome list was writen to GCF_000173355.1_ASM17335v1_genomic.fna/target_genomes.txt
[2024-01-24 12:53:47,973] [INFO] Task started: fastANI
[2024-01-24 12:53:47,974] [INFO] Running command: fastANI --query /var/lib/cwl/stgf786a989-e8ab-4771-8853-bd21666907eb/GCF_000173355.1_ASM17335v1_genomic.fna.gz --refList GCF_000173355.1_ASM17335v1_genomic.fna/target_genomes.txt --output GCF_000173355.1_ASM17335v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:53:51,745] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:51,745] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ab84521-3f55-492b-9cf5-17ebecff3c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:53:51,746] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ab84521-3f55-492b-9cf5-17ebecff3c0b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:53:51,799] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:53:51,799] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:53:51,799] [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 hydrogenalis	strain=DSM 7454	GCA_000173355.1	33029	33029	type	True	100.0	601	605	95	conclusive
Anaerococcus jeddahensis	strain=SB3	GCA_001182725.1	1673719	1673719	type	True	86.9749	458	605	95	below_threshold
Anaerococcus ihuae	strain=Marseille-Q5893	GCA_928368155.1	2899519	2899519	type	True	86.6743	451	605	95	below_threshold
Anaerococcus obesiensis	strain=ph10	GCA_000311745.1	1287640	1287640	type	True	85.851	450	605	95	below_threshold
Anaerococcus vaginalis	strain=FDAARGOS_988	GCA_016127475.1	33037	33037	type	True	85.8313	441	605	95	below_threshold
Anaerococcus vaginalis	strain=ATCC 51170	GCA_000163295.1	33037	33037	type	True	85.7895	438	605	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:53:51,801] [INFO] DFAST Taxonomy check result was written to GCF_000173355.1_ASM17335v1_genomic.fna/tc_result.tsv
[2024-01-24 12:53:51,801] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:53:51,802] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:53:51,802] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ab84521-3f55-492b-9cf5-17ebecff3c0b/dqc_reference/checkm_data
[2024-01-24 12:53:51,808] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:53:51,836] [INFO] Task started: CheckM
[2024-01-24 12:53:51,836] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000173355.1_ASM17335v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000173355.1_ASM17335v1_genomic.fna/checkm_input GCF_000173355.1_ASM17335v1_genomic.fna/checkm_result
[2024-01-24 12:54:13,288] [INFO] Task succeeded: CheckM
[2024-01-24 12:54:13,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:54:13,312] [INFO] ===== Completeness check finished =====
[2024-01-24 12:54:13,313] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:54:13,313] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000173355.1_ASM17335v1_genomic.fna/markers.fasta)
[2024-01-24 12:54:13,314] [INFO] Task started: Blastn
[2024-01-24 12:54:13,314] [INFO] Running command: blastn -query GCF_000173355.1_ASM17335v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ab84521-3f55-492b-9cf5-17ebecff3c0b/dqc_reference/reference_markers_gtdb.fasta -out GCF_000173355.1_ASM17335v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:14,159] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:14,162] [INFO] Selected 8 target genomes.
[2024-01-24 12:54:14,162] [INFO] Target genome list was writen to GCF_000173355.1_ASM17335v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:54:14,168] [INFO] Task started: fastANI
[2024-01-24 12:54:14,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgf786a989-e8ab-4771-8853-bd21666907eb/GCF_000173355.1_ASM17335v1_genomic.fna.gz --refList GCF_000173355.1_ASM17335v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000173355.1_ASM17335v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:54:18,556] [INFO] Task succeeded: fastANI
[2024-01-24 12:54:18,574] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:54:18,574] [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_000173355.1	s__Anaerococcus hydrogenalis	100.0	601	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	97.52	96.64	0.89	0.85	5	conclusive
GCA_900550345.1	s__Anaerococcus sp900550345	89.3713	305	605	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_000321005.1	s__Anaerococcus senegalensis	89.3642	466	605	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_001182725.1	s__Anaerococcus jeddahensis	86.9879	458	605	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_001487145.1	s__Anaerococcus rubeinfantis	86.4824	448	605	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_000311745.1	s__Anaerococcus obesiensis	85.8635	449	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	96.6984	97.99	96.80	0.92	0.85	6	-
GCF_000307225.1	s__Anaerococcus vaginalis_B	85.8031	436	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_018363915.1	s__Anaerococcus vaginalis_C	85.6264	425	605	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	96.5262	96.79	96.79	0.85	0.85	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:54:18,578] [INFO] GTDB search result was written to GCF_000173355.1_ASM17335v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:54:18,579] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:54:18,583] [INFO] DFAST_QC result json was written to GCF_000173355.1_ASM17335v1_genomic.fna/dqc_result.json
[2024-01-24 12:54:18,583] [INFO] DFAST_QC completed!
[2024-01-24 12:54:18,583] [INFO] Total running time: 0h0m37s