[2024-01-24 12:13:34,334] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:34,337] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:34,338] [INFO] DQC Reference Directory: /var/lib/cwl/stgf95f211a-9a62-4e15-9f04-664eceda0584/dqc_reference
[2024-01-24 12:13:35,541] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:35,542] [INFO] Task started: Prodigal
[2024-01-24 12:13:35,542] [INFO] Running command: gunzip -c /var/lib/cwl/stg41949ec6-2d78-443c-84a5-49657fb0aec4/GCF_900087015.1_PRJEB13910_genomic.fna.gz | prodigal -d GCF_900087015.1_PRJEB13910_genomic.fna/cds.fna -a GCF_900087015.1_PRJEB13910_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:43,379] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:43,381] [INFO] Task started: HMMsearch
[2024-01-24 12:13:43,381] [INFO] Running command: hmmsearch --tblout GCF_900087015.1_PRJEB13910_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf95f211a-9a62-4e15-9f04-664eceda0584/dqc_reference/reference_markers.hmm GCF_900087015.1_PRJEB13910_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:43,680] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:43,682] [INFO] Found 6/6 markers.
[2024-01-24 12:13:43,714] [INFO] Query marker FASTA was written to GCF_900087015.1_PRJEB13910_genomic.fna/markers.fasta
[2024-01-24 12:13:43,715] [INFO] Task started: Blastn
[2024-01-24 12:13:43,715] [INFO] Running command: blastn -query GCF_900087015.1_PRJEB13910_genomic.fna/markers.fasta -db /var/lib/cwl/stgf95f211a-9a62-4e15-9f04-664eceda0584/dqc_reference/reference_markers.fasta -out GCF_900087015.1_PRJEB13910_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:44,506] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:44,510] [INFO] Selected 20 target genomes.
[2024-01-24 12:13:44,510] [INFO] Target genome list was writen to GCF_900087015.1_PRJEB13910_genomic.fna/target_genomes.txt
[2024-01-24 12:13:44,635] [INFO] Task started: fastANI
[2024-01-24 12:13:44,635] [INFO] Running command: fastANI --query /var/lib/cwl/stg41949ec6-2d78-443c-84a5-49657fb0aec4/GCF_900087015.1_PRJEB13910_genomic.fna.gz --refList GCF_900087015.1_PRJEB13910_genomic.fna/target_genomes.txt --output GCF_900087015.1_PRJEB13910_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:57,706] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:57,706] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf95f211a-9a62-4e15-9f04-664eceda0584/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:57,707] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf95f211a-9a62-4e15-9f04-664eceda0584/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:57,714] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:13:57,714] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:57,714] [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
Christensenella timonensis	strain=Marseille-P2437	GCA_900087015.1	1816678	1816678	type	True	100.0	882	883	95	conclusive
Christensenella hongkongensis	strain=HKU16	GCA_000981035.1	270498	270498	type	True	79.6061	248	883	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_001571425.1	626937	626937	type	True	79.5824	229	883	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_001678855.1	626937	626937	type	True	79.5078	233	883	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_001652705.1	626937	626937	type	True	79.4954	241	883	95	below_threshold
Christensenella hongkongensis	strain=DSM 18959	GCA_004342745.1	270498	270498	type	True	79.4028	245	883	95	below_threshold
Christensenella intestinihominis	strain=AF73-05CM02	GCA_001678845.1	1851429	1851429	type	True	78.8234	227	883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:57,716] [INFO] DFAST Taxonomy check result was written to GCF_900087015.1_PRJEB13910_genomic.fna/tc_result.tsv
[2024-01-24 12:13:57,718] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:57,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:57,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf95f211a-9a62-4e15-9f04-664eceda0584/dqc_reference/checkm_data
[2024-01-24 12:13:57,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:57,753] [INFO] Task started: CheckM
[2024-01-24 12:13:57,754] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900087015.1_PRJEB13910_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900087015.1_PRJEB13910_genomic.fna/checkm_input GCF_900087015.1_PRJEB13910_genomic.fna/checkm_result
[2024-01-24 12:14:27,512] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:27,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:27,539] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:27,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:27,540] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900087015.1_PRJEB13910_genomic.fna/markers.fasta)
[2024-01-24 12:14:27,540] [INFO] Task started: Blastn
[2024-01-24 12:14:27,540] [INFO] Running command: blastn -query GCF_900087015.1_PRJEB13910_genomic.fna/markers.fasta -db /var/lib/cwl/stgf95f211a-9a62-4e15-9f04-664eceda0584/dqc_reference/reference_markers_gtdb.fasta -out GCF_900087015.1_PRJEB13910_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:28,418] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:28,421] [INFO] Selected 19 target genomes.
[2024-01-24 12:14:28,422] [INFO] Target genome list was writen to GCF_900087015.1_PRJEB13910_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:28,459] [INFO] Task started: fastANI
[2024-01-24 12:14:28,460] [INFO] Running command: fastANI --query /var/lib/cwl/stg41949ec6-2d78-443c-84a5-49657fb0aec4/GCF_900087015.1_PRJEB13910_genomic.fna.gz --refList GCF_900087015.1_PRJEB13910_genomic.fna/target_genomes_gtdb.txt --output GCF_900087015.1_PRJEB13910_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:40,755] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:40,766] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:40,767] [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_900087015.1	s__Christensenella timonensis	100.0	882	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_003628755.1	s__Christensenella minuta	79.8738	238	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	99.90	99.68	0.97	0.85	7	-
GCF_000981035.1	s__Christensenella hongkongensis	79.6061	248	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	99.51	99.03	0.96	0.95	3	-
GCA_900155415.1	s__Christensenella massiliensis	79.0585	196	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014287795.1	s__Christensenella sp014287795	78.8212	181	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001678845.1	s__Christensenella intestinihominis	78.8038	228	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	100.00	100.00	1.00	1.00	2	-
GCA_002407725.1	s__UBA5399 sp002407725	76.2863	60	883	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__UBA5399	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:40,768] [INFO] GTDB search result was written to GCF_900087015.1_PRJEB13910_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:40,769] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:40,773] [INFO] DFAST_QC result json was written to GCF_900087015.1_PRJEB13910_genomic.fna/dqc_result.json
[2024-01-24 12:14:40,774] [INFO] DFAST_QC completed!
[2024-01-24 12:14:40,774] [INFO] Total running time: 0h1m6s