[2024-01-24 14:30:33,135] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:33,138] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:33,138] [INFO] DQC Reference Directory: /var/lib/cwl/stga40d01e9-7c86-40c4-8005-99d4ef8ba5e6/dqc_reference
[2024-01-24 14:30:34,649] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:34,650] [INFO] Task started: Prodigal
[2024-01-24 14:30:34,650] [INFO] Running command: gunzip -c /var/lib/cwl/stg374b29a0-f99a-4062-b634-86796c4a288a/GCF_900626155.1_PRJEB22908_genomic.fna.gz | prodigal -d GCF_900626155.1_PRJEB22908_genomic.fna/cds.fna -a GCF_900626155.1_PRJEB22908_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:38,243] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:38,243] [INFO] Task started: HMMsearch
[2024-01-24 14:30:38,243] [INFO] Running command: hmmsearch --tblout GCF_900626155.1_PRJEB22908_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga40d01e9-7c86-40c4-8005-99d4ef8ba5e6/dqc_reference/reference_markers.hmm GCF_900626155.1_PRJEB22908_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:38,510] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:38,512] [INFO] Found 6/6 markers.
[2024-01-24 14:30:38,534] [INFO] Query marker FASTA was written to GCF_900626155.1_PRJEB22908_genomic.fna/markers.fasta
[2024-01-24 14:30:38,534] [INFO] Task started: Blastn
[2024-01-24 14:30:38,534] [INFO] Running command: blastn -query GCF_900626155.1_PRJEB22908_genomic.fna/markers.fasta -db /var/lib/cwl/stga40d01e9-7c86-40c4-8005-99d4ef8ba5e6/dqc_reference/reference_markers.fasta -out GCF_900626155.1_PRJEB22908_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:39,195] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:39,199] [INFO] Selected 10 target genomes.
[2024-01-24 14:30:39,199] [INFO] Target genome list was writen to GCF_900626155.1_PRJEB22908_genomic.fna/target_genomes.txt
[2024-01-24 14:30:39,204] [INFO] Task started: fastANI
[2024-01-24 14:30:39,204] [INFO] Running command: fastANI --query /var/lib/cwl/stg374b29a0-f99a-4062-b634-86796c4a288a/GCF_900626155.1_PRJEB22908_genomic.fna.gz --refList GCF_900626155.1_PRJEB22908_genomic.fna/target_genomes.txt --output GCF_900626155.1_PRJEB22908_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:43,865] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:43,865] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga40d01e9-7c86-40c4-8005-99d4ef8ba5e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:43,866] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga40d01e9-7c86-40c4-8005-99d4ef8ba5e6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:43,875] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:43,875] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:43,875] [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 vaginimassiliensis	strain=Marseille-P4512	GCA_900626155.1	2042308	2042308	type	True	100.0	612	612	95	conclusive
Anaerococcus prevotii	strain=NCTC11806	GCA_900445285.1	33034	33034	type	True	82.2448	311	612	95	below_threshold
Anaerococcus prevotii	strain=DSM 20548	GCA_000024105.1	33034	33034	type	True	82.2392	315	612	95	below_threshold
Anaerococcus marasmi	strain=Marseille-P3557	GCA_900290195.1	2057797	2057797	type	True	82.1452	324	612	95	below_threshold
Anaerococcus degeneri	strain=FDAARGOS_1538	GCA_020215685.1	361500	361500	type	True	81.2377	155	612	95	below_threshold
Anaerococcus tetradius	strain=ATCC 35098	GCA_000159095.1	33036	33036	type	True	81.2229	299	612	95	below_threshold
Anaerococcus ihuae	strain=Marseille-Q5893	GCA_928368155.1	2899519	2899519	type	True	81.1702	154	612	95	below_threshold
Anaerococcus degeneri	strain=DSM 29674	GCA_017874475.1	361500	361500	type	True	81.035	155	612	95	below_threshold
Anaerococcus octavius	strain=NCTC9810	GCA_900445265.1	54007	54007	type	True	79.8972	163	612	95	below_threshold
Anaerococcus vaginalis	strain=FDAARGOS_988	GCA_016127475.1	33037	33037	type	True	79.6697	137	612	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:43,877] [INFO] DFAST Taxonomy check result was written to GCF_900626155.1_PRJEB22908_genomic.fna/tc_result.tsv
[2024-01-24 14:30:43,878] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:43,878] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:43,878] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga40d01e9-7c86-40c4-8005-99d4ef8ba5e6/dqc_reference/checkm_data
[2024-01-24 14:30:43,879] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:43,904] [INFO] Task started: CheckM
[2024-01-24 14:30:43,905] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900626155.1_PRJEB22908_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900626155.1_PRJEB22908_genomic.fna/checkm_input GCF_900626155.1_PRJEB22908_genomic.fna/checkm_result
[2024-01-24 14:31:03,160] [INFO] Task succeeded: CheckM
[2024-01-24 14:31:03,162] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:31:03,180] [INFO] ===== Completeness check finished =====
[2024-01-24 14:31:03,181] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:31:03,181] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900626155.1_PRJEB22908_genomic.fna/markers.fasta)
[2024-01-24 14:31:03,182] [INFO] Task started: Blastn
[2024-01-24 14:31:03,182] [INFO] Running command: blastn -query GCF_900626155.1_PRJEB22908_genomic.fna/markers.fasta -db /var/lib/cwl/stga40d01e9-7c86-40c4-8005-99d4ef8ba5e6/dqc_reference/reference_markers_gtdb.fasta -out GCF_900626155.1_PRJEB22908_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:04,050] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:04,059] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:04,059] [INFO] Target genome list was writen to GCF_900626155.1_PRJEB22908_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:31:04,069] [INFO] Task started: fastANI
[2024-01-24 14:31:04,070] [INFO] Running command: fastANI --query /var/lib/cwl/stg374b29a0-f99a-4062-b634-86796c4a288a/GCF_900626155.1_PRJEB22908_genomic.fna.gz --refList GCF_900626155.1_PRJEB22908_genomic.fna/target_genomes_gtdb.txt --output GCF_900626155.1_PRJEB22908_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:10,410] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:10,423] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:10,423] [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_900626155.1	s__Anaerococcus vaginimassiliensis	100.0	612	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	95.85	95.85	0.94	0.94	2	conclusive
GCF_000024105.1	s__Anaerococcus prevotii	82.2292	315	612	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_900290195.1	s__Anaerococcus marasmi	82.0821	325	612	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	81.7512	175	612	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_000159095.1	s__Anaerococcus tetradius	81.2371	299	612	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_017874475.1	s__Anaerococcus degeneri	80.9859	153	612	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	80.3818	163	612	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_900445265.1	s__Anaerococcus octavius	79.9087	162	612	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_009696575.1	s__Anaerococcus porci	79.1908	108	612	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_016798225.1	s__Anaerococcus sp900541365	78.3204	139	612	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Anaerococcus	95.0	99.32	99.29	0.94	0.94	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:31:10,425] [INFO] GTDB search result was written to GCF_900626155.1_PRJEB22908_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:10,426] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:10,429] [INFO] DFAST_QC result json was written to GCF_900626155.1_PRJEB22908_genomic.fna/dqc_result.json
[2024-01-24 14:31:10,429] [INFO] DFAST_QC completed!
[2024-01-24 14:31:10,429] [INFO] Total running time: 0h0m37s