[2023-06-05 18:38:44,434] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:38:44,437] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:38:44,437] [INFO] DQC Reference Directory: /var/lib/cwl/stgb40eb2d3-b954-4e10-8828-f94aefd53215/dqc_reference
[2023-06-05 18:38:46,097] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:38:46,099] [INFO] Task started: Prodigal
[2023-06-05 18:38:46,100] [INFO] Running command: gunzip -c /var/lib/cwl/stg362371e4-48d6-4d7c-a8c9-9de9854a648a/GCA_004172855.1_ASM417285v1_genomic.fna.gz | prodigal -d GCA_004172855.1_ASM417285v1_genomic.fna/cds.fna -a GCA_004172855.1_ASM417285v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:38:53,876] [INFO] Task succeeded: Prodigal
[2023-06-05 18:38:53,877] [INFO] Task started: HMMsearch
[2023-06-05 18:38:53,877] [INFO] Running command: hmmsearch --tblout GCA_004172855.1_ASM417285v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb40eb2d3-b954-4e10-8828-f94aefd53215/dqc_reference/reference_markers.hmm GCA_004172855.1_ASM417285v1_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:38:54,043] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:38:54,044] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg362371e4-48d6-4d7c-a8c9-9de9854a648a/GCA_004172855.1_ASM417285v1_genomic.fna.gz]
[2023-06-05 18:38:54,073] [INFO] Query marker FASTA was written to GCA_004172855.1_ASM417285v1_genomic.fna/markers.fasta
[2023-06-05 18:38:54,074] [INFO] Task started: Blastn
[2023-06-05 18:38:54,074] [INFO] Running command: blastn -query GCA_004172855.1_ASM417285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb40eb2d3-b954-4e10-8828-f94aefd53215/dqc_reference/reference_markers.fasta -out GCA_004172855.1_ASM417285v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:38:54,641] [INFO] Task succeeded: Blastn
[2023-06-05 18:38:54,644] [INFO] Selected 19 target genomes.
[2023-06-05 18:38:54,645] [INFO] Target genome list was writen to GCA_004172855.1_ASM417285v1_genomic.fna/target_genomes.txt
[2023-06-05 18:38:54,650] [INFO] Task started: fastANI
[2023-06-05 18:38:54,651] [INFO] Running command: fastANI --query /var/lib/cwl/stg362371e4-48d6-4d7c-a8c9-9de9854a648a/GCA_004172855.1_ASM417285v1_genomic.fna.gz --refList GCA_004172855.1_ASM417285v1_genomic.fna/target_genomes.txt --output GCA_004172855.1_ASM417285v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:39:11,512] [INFO] Task succeeded: fastANI
[2023-06-05 18:39:11,513] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb40eb2d3-b954-4e10-8828-f94aefd53215/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:39:11,513] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb40eb2d3-b954-4e10-8828-f94aefd53215/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:39:11,517] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:39:11,517] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:39:11,517] [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
Mucilaginibacter arboris	strain=HMF7410	GCA_009754915.1	2682090	2682090	type	True	78.6906	141	426	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:39:11,519] [INFO] DFAST Taxonomy check result was written to GCA_004172855.1_ASM417285v1_genomic.fna/tc_result.tsv
[2023-06-05 18:39:11,519] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:39:11,519] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:39:11,519] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb40eb2d3-b954-4e10-8828-f94aefd53215/dqc_reference/checkm_data
[2023-06-05 18:39:11,520] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:39:11,547] [INFO] Task started: CheckM
[2023-06-05 18:39:11,547] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_004172855.1_ASM417285v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_004172855.1_ASM417285v1_genomic.fna/checkm_input GCA_004172855.1_ASM417285v1_genomic.fna/checkm_result
[2023-06-05 18:39:37,557] [INFO] Task succeeded: CheckM
[2023-06-05 18:39:37,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 12.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:39:37,614] [INFO] ===== Completeness check finished =====
[2023-06-05 18:39:37,614] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:39:37,615] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_004172855.1_ASM417285v1_genomic.fna/markers.fasta)
[2023-06-05 18:39:37,615] [INFO] Task started: Blastn
[2023-06-05 18:39:37,615] [INFO] Running command: blastn -query GCA_004172855.1_ASM417285v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb40eb2d3-b954-4e10-8828-f94aefd53215/dqc_reference/reference_markers_gtdb.fasta -out GCA_004172855.1_ASM417285v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:39:38,077] [INFO] Task succeeded: Blastn
[2023-06-05 18:39:38,080] [INFO] Selected 18 target genomes.
[2023-06-05 18:39:38,080] [INFO] Target genome list was writen to GCA_004172855.1_ASM417285v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:39:38,127] [INFO] Task started: fastANI
[2023-06-05 18:39:38,128] [INFO] Running command: fastANI --query /var/lib/cwl/stg362371e4-48d6-4d7c-a8c9-9de9854a648a/GCA_004172855.1_ASM417285v1_genomic.fna.gz --refList GCA_004172855.1_ASM417285v1_genomic.fna/target_genomes_gtdb.txt --output GCA_004172855.1_ASM417285v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:39:51,803] [INFO] Task succeeded: fastANI
[2023-06-05 18:39:51,807] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-05 18:39:51,807] [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
GCA_903642215.1	s__Mucilaginibacter_A sp903642215	79.528	167	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009754915.1	s__Mucilaginibacter_A arboris	78.7508	139	426	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Sphingobacteriales;f__Sphingobacteriaceae;g__Mucilaginibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:39:51,809] [INFO] GTDB search result was written to GCA_004172855.1_ASM417285v1_genomic.fna/result_gtdb.tsv
[2023-06-05 18:39:51,809] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:39:51,811] [INFO] DFAST_QC result json was written to GCA_004172855.1_ASM417285v1_genomic.fna/dqc_result.json
[2023-06-05 18:39:51,811] [INFO] DFAST_QC completed!
[2023-06-05 18:39:51,811] [INFO] Total running time: 0h1m7s