[2024-01-24 14:37:46,904] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:37:46,906] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:37:46,907] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2c30d26-ee53-43d1-acec-87cb8695654a/dqc_reference
[2024-01-24 14:37:50,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:37:50,280] [INFO] Task started: Prodigal
[2024-01-24 14:37:50,281] [INFO] Running command: gunzip -c /var/lib/cwl/stgd9a96baf-e0fc-4341-8a30-6c86807d347e/GCF_004342745.1_ASM434274v1_genomic.fna.gz | prodigal -d GCF_004342745.1_ASM434274v1_genomic.fna/cds.fna -a GCF_004342745.1_ASM434274v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:37:59,277] [INFO] Task succeeded: Prodigal
[2024-01-24 14:37:59,278] [INFO] Task started: HMMsearch
[2024-01-24 14:37:59,278] [INFO] Running command: hmmsearch --tblout GCF_004342745.1_ASM434274v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2c30d26-ee53-43d1-acec-87cb8695654a/dqc_reference/reference_markers.hmm GCF_004342745.1_ASM434274v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:37:59,546] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:37:59,547] [INFO] Found 6/6 markers.
[2024-01-24 14:37:59,585] [INFO] Query marker FASTA was written to GCF_004342745.1_ASM434274v1_genomic.fna/markers.fasta
[2024-01-24 14:37:59,586] [INFO] Task started: Blastn
[2024-01-24 14:37:59,586] [INFO] Running command: blastn -query GCF_004342745.1_ASM434274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2c30d26-ee53-43d1-acec-87cb8695654a/dqc_reference/reference_markers.fasta -out GCF_004342745.1_ASM434274v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:00,218] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:00,224] [INFO] Selected 15 target genomes.
[2024-01-24 14:38:00,225] [INFO] Target genome list was writen to GCF_004342745.1_ASM434274v1_genomic.fna/target_genomes.txt
[2024-01-24 14:38:00,244] [INFO] Task started: fastANI
[2024-01-24 14:38:00,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a96baf-e0fc-4341-8a30-6c86807d347e/GCF_004342745.1_ASM434274v1_genomic.fna.gz --refList GCF_004342745.1_ASM434274v1_genomic.fna/target_genomes.txt --output GCF_004342745.1_ASM434274v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:38:11,404] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:11,404] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2c30d26-ee53-43d1-acec-87cb8695654a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:38:11,405] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2c30d26-ee53-43d1-acec-87cb8695654a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:38:11,412] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:38:11,412] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:38:11,412] [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 hongkongensis	strain=DSM 18959	GCA_004342745.1	270498	270498	type	True	100.0	1028	1031	95	conclusive
Christensenella hongkongensis	strain=HKU16	GCA_000981035.1	270498	270498	type	True	99.9653	1014	1031	95	conclusive
Christensenella minuta	strain=DSM 22607	GCA_001652705.1	626937	626937	type	True	79.8152	261	1031	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_001678855.1	626937	626937	type	True	79.7913	261	1031	95	below_threshold
Christensenella minuta	strain=DSM 22607	GCA_001571425.1	626937	626937	type	True	79.629	257	1031	95	below_threshold
Christensenella timonensis	strain=Marseille-P2437	GCA_900087015.1	1816678	1816678	type	True	79.468	242	1031	95	below_threshold
Christensenella intestinihominis	strain=AF73-05CM02	GCA_001678845.1	1851429	1851429	type	True	78.7163	279	1031	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:38:11,414] [INFO] DFAST Taxonomy check result was written to GCF_004342745.1_ASM434274v1_genomic.fna/tc_result.tsv
[2024-01-24 14:38:11,415] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:38:11,415] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:38:11,415] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2c30d26-ee53-43d1-acec-87cb8695654a/dqc_reference/checkm_data
[2024-01-24 14:38:11,416] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:38:11,451] [INFO] Task started: CheckM
[2024-01-24 14:38:11,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004342745.1_ASM434274v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004342745.1_ASM434274v1_genomic.fna/checkm_input GCF_004342745.1_ASM434274v1_genomic.fna/checkm_result
[2024-01-24 14:38:43,201] [INFO] Task succeeded: CheckM
[2024-01-24 14:38:43,202] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:38:43,220] [INFO] ===== Completeness check finished =====
[2024-01-24 14:38:43,221] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:38:43,222] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004342745.1_ASM434274v1_genomic.fna/markers.fasta)
[2024-01-24 14:38:43,222] [INFO] Task started: Blastn
[2024-01-24 14:38:43,222] [INFO] Running command: blastn -query GCF_004342745.1_ASM434274v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2c30d26-ee53-43d1-acec-87cb8695654a/dqc_reference/reference_markers_gtdb.fasta -out GCF_004342745.1_ASM434274v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:38:44,024] [INFO] Task succeeded: Blastn
[2024-01-24 14:38:44,029] [INFO] Selected 16 target genomes.
[2024-01-24 14:38:44,029] [INFO] Target genome list was writen to GCF_004342745.1_ASM434274v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:38:44,044] [INFO] Task started: fastANI
[2024-01-24 14:38:44,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgd9a96baf-e0fc-4341-8a30-6c86807d347e/GCF_004342745.1_ASM434274v1_genomic.fna.gz --refList GCF_004342745.1_ASM434274v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004342745.1_ASM434274v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:38:53,593] [INFO] Task succeeded: fastANI
[2024-01-24 14:38:53,599] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:38:53,600] [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_000981035.1	s__Christensenella hongkongensis	99.9653	1014	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	99.51	99.03	0.96	0.95	3	conclusive
GCF_003628755.1	s__Christensenella minuta	79.7387	262	1031	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_900087015.1	s__Christensenella timonensis	79.468	242	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014287795.1	s__Christensenella sp014287795	79.3163	242	1031	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	78.701	280	1031	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_900155415.1	s__Christensenella massiliensis	77.7864	194	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:38:53,601] [INFO] GTDB search result was written to GCF_004342745.1_ASM434274v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:38:53,602] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:38:53,605] [INFO] DFAST_QC result json was written to GCF_004342745.1_ASM434274v1_genomic.fna/dqc_result.json
[2024-01-24 14:38:53,605] [INFO] DFAST_QC completed!
[2024-01-24 14:38:53,605] [INFO] Total running time: 0h1m7s