[2024-01-25 20:22:05,642] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:22:05,643] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:22:05,644] [INFO] DQC Reference Directory: /var/lib/cwl/stg0462e700-9764-410c-bf4c-1ed6d6c9664d/dqc_reference
[2024-01-25 20:22:06,867] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:22:06,868] [INFO] Task started: Prodigal
[2024-01-25 20:22:06,868] [INFO] Running command: gunzip -c /var/lib/cwl/stg7f98587d-2407-400c-9077-a0104ce45cf2/GCF_017874535.1_ASM1787453v1_genomic.fna.gz | prodigal -d GCF_017874535.1_ASM1787453v1_genomic.fna/cds.fna -a GCF_017874535.1_ASM1787453v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:22:09,314] [INFO] Task succeeded: Prodigal
[2024-01-25 20:22:09,314] [INFO] Task started: HMMsearch
[2024-01-25 20:22:09,314] [INFO] Running command: hmmsearch --tblout GCF_017874535.1_ASM1787453v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0462e700-9764-410c-bf4c-1ed6d6c9664d/dqc_reference/reference_markers.hmm GCF_017874535.1_ASM1787453v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:22:09,511] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:22:09,512] [INFO] Found 6/6 markers.
[2024-01-25 20:22:09,529] [INFO] Query marker FASTA was written to GCF_017874535.1_ASM1787453v1_genomic.fna/markers.fasta
[2024-01-25 20:22:09,529] [INFO] Task started: Blastn
[2024-01-25 20:22:09,529] [INFO] Running command: blastn -query GCF_017874535.1_ASM1787453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0462e700-9764-410c-bf4c-1ed6d6c9664d/dqc_reference/reference_markers.fasta -out GCF_017874535.1_ASM1787453v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:10,072] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:10,082] [INFO] Selected 11 target genomes.
[2024-01-25 20:22:10,082] [INFO] Target genome list was writen to GCF_017874535.1_ASM1787453v1_genomic.fna/target_genomes.txt
[2024-01-25 20:22:10,094] [INFO] Task started: fastANI
[2024-01-25 20:22:10,094] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f98587d-2407-400c-9077-a0104ce45cf2/GCF_017874535.1_ASM1787453v1_genomic.fna.gz --refList GCF_017874535.1_ASM1787453v1_genomic.fna/target_genomes.txt --output GCF_017874535.1_ASM1787453v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:22:13,906] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:13,907] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0462e700-9764-410c-bf4c-1ed6d6c9664d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:22:13,907] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0462e700-9764-410c-bf4c-1ed6d6c9664d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:22:13,915] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:22:13,915] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:22:13,915] [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 nagyae	strain=DSM 101193	GCA_017874535.1	1755241	1755241	type	True	100.0	576	577	95	conclusive
Anaerococcus octavius	strain=NCTC9810	GCA_900445265.1	54007	54007	type	True	81.8036	317	577	95	below_threshold
Anaerococcus provencensis	strain=9402080	GCA_000312365.2	938293	938293	type	True	79.6923	228	577	95	below_threshold
Anaerococcus urinomassiliensis	strain=Marseille-P2143	GCA_900128425.1	1745712	1745712	type	True	79.6315	242	577	95	below_threshold
Anaerococcus vaginimassiliensis	strain=Marseille-P4512	GCA_900626155.1	2042308	2042308	type	True	78.1162	141	577	95	below_threshold
Anaerococcus ihuae	strain=Marseille-Q5893	GCA_928368155.1	2899519	2899519	type	True	77.8874	112	577	95	below_threshold
Anaerococcus tetradius	strain=ATCC 35098	GCA_000159095.1	33036	33036	type	True	77.7867	119	577	95	below_threshold
Anaerococcus vaginalis	strain=FDAARGOS_988	GCA_016127475.1	33037	33037	type	True	77.5727	103	577	95	below_threshold
Anaerococcus jeddahensis	strain=SB3	GCA_001182725.1	1673719	1673719	type	True	77.4769	103	577	95	below_threshold
Anaerococcus degeneri	strain=FDAARGOS_1538	GCA_020215685.1	361500	361500	type	True	77.4463	95	577	95	below_threshold
Anaerococcus vaginalis	strain=ATCC 51170	GCA_000163295.1	33037	33037	type	True	77.2897	104	577	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:22:13,916] [INFO] DFAST Taxonomy check result was written to GCF_017874535.1_ASM1787453v1_genomic.fna/tc_result.tsv
[2024-01-25 20:22:13,917] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:22:13,917] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:22:13,917] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0462e700-9764-410c-bf4c-1ed6d6c9664d/dqc_reference/checkm_data
[2024-01-25 20:22:13,918] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:22:13,938] [INFO] Task started: CheckM
[2024-01-25 20:22:13,938] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017874535.1_ASM1787453v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017874535.1_ASM1787453v1_genomic.fna/checkm_input GCF_017874535.1_ASM1787453v1_genomic.fna/checkm_result
[2024-01-25 20:22:28,136] [INFO] Task succeeded: CheckM
[2024-01-25 20:22:28,140] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:22:28,164] [INFO] ===== Completeness check finished =====
[2024-01-25 20:22:28,164] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:22:28,164] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017874535.1_ASM1787453v1_genomic.fna/markers.fasta)
[2024-01-25 20:22:28,165] [INFO] Task started: Blastn
[2024-01-25 20:22:28,165] [INFO] Running command: blastn -query GCF_017874535.1_ASM1787453v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0462e700-9764-410c-bf4c-1ed6d6c9664d/dqc_reference/reference_markers_gtdb.fasta -out GCF_017874535.1_ASM1787453v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:22:28,889] [INFO] Task succeeded: Blastn
[2024-01-25 20:22:28,891] [INFO] Selected 13 target genomes.
[2024-01-25 20:22:28,892] [INFO] Target genome list was writen to GCF_017874535.1_ASM1787453v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:22:28,905] [INFO] Task started: fastANI
[2024-01-25 20:22:28,905] [INFO] Running command: fastANI --query /var/lib/cwl/stg7f98587d-2407-400c-9077-a0104ce45cf2/GCF_017874535.1_ASM1787453v1_genomic.fna.gz --refList GCF_017874535.1_ASM1787453v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017874535.1_ASM1787453v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:22:33,126] [INFO] Task succeeded: fastANI
[2024-01-25 20:22:33,133] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:22:33,134] [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_017874535.1	s__Anaerococcus nagyae	100.0	576	577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.14	98.91	0.93	0.91	5	conclusive
GCF_900445265.1	s__Anaerococcus octavius	81.7813	317	577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	98.32	98.32	0.89	0.88	3	-
GCF_016798225.1	s__Anaerococcus sp900541365	80.0258	265	577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.32	99.29	0.94	0.94	3	-
GCF_000312365.2	s__Anaerococcus provencensis	79.6905	228	577	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_900128425.1	s__Anaerococcus urinomassiliensis	79.6079	243	577	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_900232825.1	s__Anaerococcus sp900232825	78.5552	179	577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	95.02	95.02	0.81	0.81	2	-
GCF_009696575.1	s__Anaerococcus porci	78.0263	94	577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.45	99.45	0.91	0.91	2	-
GCF_000321005.1	s__Anaerococcus senegalensis	77.7874	109	577	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_000159095.1	s__Anaerococcus tetradius	77.7867	119	577	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_001487145.1	s__Anaerococcus rubeinfantis	77.2912	112	577	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:22:33,135] [INFO] GTDB search result was written to GCF_017874535.1_ASM1787453v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:22:33,136] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:22:33,140] [INFO] DFAST_QC result json was written to GCF_017874535.1_ASM1787453v1_genomic.fna/dqc_result.json
[2024-01-25 20:22:33,140] [INFO] DFAST_QC completed!
[2024-01-25 20:22:33,140] [INFO] Total running time: 0h0m27s