[2024-01-24 13:57:31,921] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:31,923] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:31,923] [INFO] DQC Reference Directory: /var/lib/cwl/stgc0b927ff-099e-4fe4-885f-7d6a7dca431b/dqc_reference
[2024-01-24 13:57:33,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:33,241] [INFO] Task started: Prodigal
[2024-01-24 13:57:33,241] [INFO] Running command: gunzip -c /var/lib/cwl/stg26cc856c-1291-4e15-9e4f-950306cc6241/GCF_007830435.1_ASM783043v1_genomic.fna.gz | prodigal -d GCF_007830435.1_ASM783043v1_genomic.fna/cds.fna -a GCF_007830435.1_ASM783043v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:45,221] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:45,221] [INFO] Task started: HMMsearch
[2024-01-24 13:57:45,222] [INFO] Running command: hmmsearch --tblout GCF_007830435.1_ASM783043v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc0b927ff-099e-4fe4-885f-7d6a7dca431b/dqc_reference/reference_markers.hmm GCF_007830435.1_ASM783043v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:45,541] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:45,547] [INFO] Found 6/6 markers.
[2024-01-24 13:57:45,579] [INFO] Query marker FASTA was written to GCF_007830435.1_ASM783043v1_genomic.fna/markers.fasta
[2024-01-24 13:57:45,580] [INFO] Task started: Blastn
[2024-01-24 13:57:45,580] [INFO] Running command: blastn -query GCF_007830435.1_ASM783043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0b927ff-099e-4fe4-885f-7d6a7dca431b/dqc_reference/reference_markers.fasta -out GCF_007830435.1_ASM783043v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:57:46,265] [INFO] Task succeeded: Blastn
[2024-01-24 13:57:46,268] [INFO] Selected 20 target genomes.
[2024-01-24 13:57:46,268] [INFO] Target genome list was writen to GCF_007830435.1_ASM783043v1_genomic.fna/target_genomes.txt
[2024-01-24 13:57:46,275] [INFO] Task started: fastANI
[2024-01-24 13:57:46,275] [INFO] Running command: fastANI --query /var/lib/cwl/stg26cc856c-1291-4e15-9e4f-950306cc6241/GCF_007830435.1_ASM783043v1_genomic.fna.gz --refList GCF_007830435.1_ASM783043v1_genomic.fna/target_genomes.txt --output GCF_007830435.1_ASM783043v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:05,863] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:05,864] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc0b927ff-099e-4fe4-885f-7d6a7dca431b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:05,864] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc0b927ff-099e-4fe4-885f-7d6a7dca431b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:05,870] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:58:05,870] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:05,870] [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
Desulfobotulus alkaliphilus	strain=ASO4-4	GCA_007830435.1	622671	622671	type	True	100.0	1285	1291	95	conclusive
Desulfobotulus mexicanus	strain=PAR22N	GCA_006175995.1	2586642	2586642	type	True	88.7069	1003	1291	95	below_threshold
Desulfoluna spongiiphila	strain=AA1	GCA_900101345.1	419481	419481	type	True	75.3912	50	1291	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:58:05,872] [INFO] DFAST Taxonomy check result was written to GCF_007830435.1_ASM783043v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:05,872] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:05,872] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:05,873] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc0b927ff-099e-4fe4-885f-7d6a7dca431b/dqc_reference/checkm_data
[2024-01-24 13:58:05,874] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:05,914] [INFO] Task started: CheckM
[2024-01-24 13:58:05,914] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007830435.1_ASM783043v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007830435.1_ASM783043v1_genomic.fna/checkm_input GCF_007830435.1_ASM783043v1_genomic.fna/checkm_result
[2024-01-24 13:58:45,846] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:45,848] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:45,866] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:45,866] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:45,866] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007830435.1_ASM783043v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:45,867] [INFO] Task started: Blastn
[2024-01-24 13:58:45,867] [INFO] Running command: blastn -query GCF_007830435.1_ASM783043v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc0b927ff-099e-4fe4-885f-7d6a7dca431b/dqc_reference/reference_markers_gtdb.fasta -out GCF_007830435.1_ASM783043v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:47,070] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:47,074] [INFO] Selected 21 target genomes.
[2024-01-24 13:58:47,074] [INFO] Target genome list was writen to GCF_007830435.1_ASM783043v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:47,125] [INFO] Task started: fastANI
[2024-01-24 13:58:47,126] [INFO] Running command: fastANI --query /var/lib/cwl/stg26cc856c-1291-4e15-9e4f-950306cc6241/GCF_007830435.1_ASM783043v1_genomic.fna.gz --refList GCF_007830435.1_ASM783043v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007830435.1_ASM783043v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:59:05,271] [INFO] Task succeeded: fastANI
[2024-01-24 13:59:05,276] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:59:05,277] [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_007830435.1	s__Desulfobotulus alkaliphilus	100.0	1285	1291	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulforegulaceae;g__Desulfobotulus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_006175995.1	s__Desulfobotulus mexicanus	88.7525	1000	1291	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulforegulaceae;g__Desulfobotulus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900699765.1	s__Desulfoluna butyratoxydans	75.8941	58	1291	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfolunaceae;g__Desulfoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002748835.1	s__GCA-2748835 sp002748835	75.8331	52	1291	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__GCA-2748835;g__GCA-2748835	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900101345.1	s__Desulfoluna spongiiphila	75.3912	50	1291	d__Bacteria;p__Desulfobacterota;c__Desulfobacteria;o__Desulfobacterales;f__Desulfolunaceae;g__Desulfoluna	95.0	98.60	98.60	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:59:05,278] [INFO] GTDB search result was written to GCF_007830435.1_ASM783043v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:59:05,279] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:59:05,281] [INFO] DFAST_QC result json was written to GCF_007830435.1_ASM783043v1_genomic.fna/dqc_result.json
[2024-01-24 13:59:05,281] [INFO] DFAST_QC completed!
[2024-01-24 13:59:05,282] [INFO] Total running time: 0h1m33s