[2024-01-24 11:51:24,654] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:51:24,658] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:51:24,658] [INFO] DQC Reference Directory: /var/lib/cwl/stgcb014305-ddc6-4450-ad57-2662f4d0990a/dqc_reference
[2024-01-24 11:51:26,049] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:51:26,050] [INFO] Task started: Prodigal
[2024-01-24 11:51:26,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg528b4a93-b0d0-4636-be4b-0ec6ca1e05b9/GCF_003628755.1_ASM362875v1_genomic.fna.gz | prodigal -d GCF_003628755.1_ASM362875v1_genomic.fna/cds.fna -a GCF_003628755.1_ASM362875v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:51:34,729] [INFO] Task succeeded: Prodigal
[2024-01-24 11:51:34,729] [INFO] Task started: HMMsearch
[2024-01-24 11:51:34,729] [INFO] Running command: hmmsearch --tblout GCF_003628755.1_ASM362875v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgcb014305-ddc6-4450-ad57-2662f4d0990a/dqc_reference/reference_markers.hmm GCF_003628755.1_ASM362875v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:51:35,040] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:51:35,041] [INFO] Found 6/6 markers.
[2024-01-24 11:51:35,073] [INFO] Query marker FASTA was written to GCF_003628755.1_ASM362875v1_genomic.fna/markers.fasta
[2024-01-24 11:51:35,074] [INFO] Task started: Blastn
[2024-01-24 11:51:35,074] [INFO] Running command: blastn -query GCF_003628755.1_ASM362875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb014305-ddc6-4450-ad57-2662f4d0990a/dqc_reference/reference_markers.fasta -out GCF_003628755.1_ASM362875v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:51:35,659] [INFO] Task succeeded: Blastn
[2024-01-24 11:51:35,664] [INFO] Selected 11 target genomes.
[2024-01-24 11:51:35,664] [INFO] Target genome list was writen to GCF_003628755.1_ASM362875v1_genomic.fna/target_genomes.txt
[2024-01-24 11:51:35,670] [INFO] Task started: fastANI
[2024-01-24 11:51:35,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg528b4a93-b0d0-4636-be4b-0ec6ca1e05b9/GCF_003628755.1_ASM362875v1_genomic.fna.gz --refList GCF_003628755.1_ASM362875v1_genomic.fna/target_genomes.txt --output GCF_003628755.1_ASM362875v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:51:44,993] [INFO] Task succeeded: fastANI
[2024-01-24 11:51:44,994] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgcb014305-ddc6-4450-ad57-2662f4d0990a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:51:44,994] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgcb014305-ddc6-4450-ad57-2662f4d0990a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:51:45,005] [INFO] Found 5 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 11:51:45,006] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:51:45,006] [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 minuta	strain=DSM 22607	GCA_003628755.1	626937	626937	type	True	100.0	986	989	95	conclusive
Christensenella minuta	strain=DSM 22607	GCA_001652705.1	626937	626937	type	True	99.9703	954	989	95	conclusive
Christensenella minuta	strain=DSM 22607	GCA_001678855.1	626937	626937	type	True	99.9698	951	989	95	conclusive
Christensenella minuta	strain=DSM 22607	GCA_001571425.1	626937	626937	type	True	99.9665	938	989	95	conclusive
Christensenella intestinihominis	strain=AF73-05CM02	GCA_001678845.1	1851429	1851429	type	True	83.5134	683	989	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:51:45,010] [INFO] DFAST Taxonomy check result was written to GCF_003628755.1_ASM362875v1_genomic.fna/tc_result.tsv
[2024-01-24 11:51:45,011] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:51:45,011] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:51:45,011] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgcb014305-ddc6-4450-ad57-2662f4d0990a/dqc_reference/checkm_data
[2024-01-24 11:51:45,014] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:51:45,049] [INFO] Task started: CheckM
[2024-01-24 11:51:45,049] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003628755.1_ASM362875v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003628755.1_ASM362875v1_genomic.fna/checkm_input GCF_003628755.1_ASM362875v1_genomic.fna/checkm_result
[2024-01-24 11:52:16,239] [INFO] Task succeeded: CheckM
[2024-01-24 11:52:16,241] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:52:16,264] [INFO] ===== Completeness check finished =====
[2024-01-24 11:52:16,265] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:52:16,265] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003628755.1_ASM362875v1_genomic.fna/markers.fasta)
[2024-01-24 11:52:16,266] [INFO] Task started: Blastn
[2024-01-24 11:52:16,266] [INFO] Running command: blastn -query GCF_003628755.1_ASM362875v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgcb014305-ddc6-4450-ad57-2662f4d0990a/dqc_reference/reference_markers_gtdb.fasta -out GCF_003628755.1_ASM362875v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:52:17,191] [INFO] Task succeeded: Blastn
[2024-01-24 11:52:17,194] [INFO] Selected 14 target genomes.
[2024-01-24 11:52:17,194] [INFO] Target genome list was writen to GCF_003628755.1_ASM362875v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:52:17,220] [INFO] Task started: fastANI
[2024-01-24 11:52:17,221] [INFO] Running command: fastANI --query /var/lib/cwl/stg528b4a93-b0d0-4636-be4b-0ec6ca1e05b9/GCF_003628755.1_ASM362875v1_genomic.fna.gz --refList GCF_003628755.1_ASM362875v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003628755.1_ASM362875v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:52:25,235] [INFO] Task succeeded: fastANI
[2024-01-24 11:52:25,248] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:52:25,248] [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_003628755.1	s__Christensenella minuta	100.0	986	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	99.90	99.68	0.97	0.85	7	conclusive
GCF_014287795.1	s__Christensenella sp014287795	83.7992	602	989	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	83.5134	683	989	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	80.2526	401	989	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_000981035.1	s__Christensenella hongkongensis	80.1067	271	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	99.51	99.03	0.96	0.95	3	-
GCF_900087015.1	s__Christensenella timonensis	79.9601	230	989	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__Christensenellaceae;g__Christensenella	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:52:25,250] [INFO] GTDB search result was written to GCF_003628755.1_ASM362875v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:52:25,251] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:52:25,254] [INFO] DFAST_QC result json was written to GCF_003628755.1_ASM362875v1_genomic.fna/dqc_result.json
[2024-01-24 11:52:25,254] [INFO] DFAST_QC completed!
[2024-01-24 11:52:25,254] [INFO] Total running time: 0h1m1s