[2024-01-24 13:40:55,430] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:55,432] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:55,432] [INFO] DQC Reference Directory: /var/lib/cwl/stga4e8b59b-607a-42a4-bb21-def4f021eada/dqc_reference
[2024-01-24 13:40:56,648] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:56,649] [INFO] Task started: Prodigal
[2024-01-24 13:40:56,649] [INFO] Running command: gunzip -c /var/lib/cwl/stgcb74d46d-e7e8-4829-9810-bc1487c4f6a4/GCF_002207765.1_ASM220776v1_genomic.fna.gz | prodigal -d GCF_002207765.1_ASM220776v1_genomic.fna/cds.fna -a GCF_002207765.1_ASM220776v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:02,472] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:02,473] [INFO] Task started: HMMsearch
[2024-01-24 13:41:02,473] [INFO] Running command: hmmsearch --tblout GCF_002207765.1_ASM220776v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga4e8b59b-607a-42a4-bb21-def4f021eada/dqc_reference/reference_markers.hmm GCF_002207765.1_ASM220776v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:02,764] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:02,765] [INFO] Found 6/6 markers.
[2024-01-24 13:41:02,788] [INFO] Query marker FASTA was written to GCF_002207765.1_ASM220776v1_genomic.fna/markers.fasta
[2024-01-24 13:41:02,788] [INFO] Task started: Blastn
[2024-01-24 13:41:02,788] [INFO] Running command: blastn -query GCF_002207765.1_ASM220776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4e8b59b-607a-42a4-bb21-def4f021eada/dqc_reference/reference_markers.fasta -out GCF_002207765.1_ASM220776v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:03,359] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:03,361] [INFO] Selected 16 target genomes.
[2024-01-24 13:41:03,362] [INFO] Target genome list was writen to GCF_002207765.1_ASM220776v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:03,373] [INFO] Task started: fastANI
[2024-01-24 13:41:03,373] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb74d46d-e7e8-4829-9810-bc1487c4f6a4/GCF_002207765.1_ASM220776v1_genomic.fna.gz --refList GCF_002207765.1_ASM220776v1_genomic.fna/target_genomes.txt --output GCF_002207765.1_ASM220776v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:13,263] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:13,264] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga4e8b59b-607a-42a4-bb21-def4f021eada/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:13,264] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga4e8b59b-607a-42a4-bb21-def4f021eada/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:13,267] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:41:13,267] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:41:13,267] [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
Calderihabitans maritimus	strain=KKC1	GCA_002207765.1	1246530	1246530	type	True	100.0	960	964	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:41:13,269] [INFO] DFAST Taxonomy check result was written to GCF_002207765.1_ASM220776v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:13,269] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:13,269] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:13,269] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga4e8b59b-607a-42a4-bb21-def4f021eada/dqc_reference/checkm_data
[2024-01-24 13:41:13,270] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:13,301] [INFO] Task started: CheckM
[2024-01-24 13:41:13,301] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002207765.1_ASM220776v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002207765.1_ASM220776v1_genomic.fna/checkm_input GCF_002207765.1_ASM220776v1_genomic.fna/checkm_result
[2024-01-24 13:41:35,192] [INFO] Task succeeded: CheckM
[2024-01-24 13:41:35,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:41:35,256] [INFO] ===== Completeness check finished =====
[2024-01-24 13:41:35,256] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:41:35,257] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002207765.1_ASM220776v1_genomic.fna/markers.fasta)
[2024-01-24 13:41:35,257] [INFO] Task started: Blastn
[2024-01-24 13:41:35,257] [INFO] Running command: blastn -query GCF_002207765.1_ASM220776v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga4e8b59b-607a-42a4-bb21-def4f021eada/dqc_reference/reference_markers_gtdb.fasta -out GCF_002207765.1_ASM220776v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:36,024] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:36,027] [INFO] Selected 22 target genomes.
[2024-01-24 13:41:36,027] [INFO] Target genome list was writen to GCF_002207765.1_ASM220776v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:41:36,376] [INFO] Task started: fastANI
[2024-01-24 13:41:36,376] [INFO] Running command: fastANI --query /var/lib/cwl/stgcb74d46d-e7e8-4829-9810-bc1487c4f6a4/GCF_002207765.1_ASM220776v1_genomic.fna.gz --refList GCF_002207765.1_ASM220776v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002207765.1_ASM220776v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:41:48,548] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:48,551] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:41:48,551] [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_002207765.1	s__Calderihabitans maritimus	100.0	960	964	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__Calderihabitantales;f__Calderihabitantaceae;g__Calderihabitans	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_017656305.1	s__JACDOG01 sp017656305	79.8772	57	964	d__Bacteria;p__Firmicutes_B;c__Moorellia;o__JADQBR01;f__JADQBR01;g__JACDOG01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:41:48,552] [INFO] GTDB search result was written to GCF_002207765.1_ASM220776v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:41:48,553] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:41:48,554] [INFO] DFAST_QC result json was written to GCF_002207765.1_ASM220776v1_genomic.fna/dqc_result.json
[2024-01-24 13:41:48,555] [INFO] DFAST_QC completed!
[2024-01-24 13:41:48,555] [INFO] Total running time: 0h0m53s