[2024-01-24 12:37:24,986] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:24,988] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:24,989] [INFO] DQC Reference Directory: /var/lib/cwl/stgddc83a59-b242-4fad-a3c1-d74e9ecc697b/dqc_reference
[2024-01-24 12:37:26,338] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,339] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,339] [INFO] Running command: gunzip -c /var/lib/cwl/stg49414d62-f238-46c4-8541-a50cd5d257f5/GCF_010120715.1_ASM1012071v1_genomic.fna.gz | prodigal -d GCF_010120715.1_ASM1012071v1_genomic.fna/cds.fna -a GCF_010120715.1_ASM1012071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:33,670] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:33,670] [INFO] Task started: HMMsearch
[2024-01-24 12:37:33,671] [INFO] Running command: hmmsearch --tblout GCF_010120715.1_ASM1012071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgddc83a59-b242-4fad-a3c1-d74e9ecc697b/dqc_reference/reference_markers.hmm GCF_010120715.1_ASM1012071v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:33,942] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:33,943] [INFO] Found 6/6 markers.
[2024-01-24 12:37:33,972] [INFO] Query marker FASTA was written to GCF_010120715.1_ASM1012071v1_genomic.fna/markers.fasta
[2024-01-24 12:37:33,973] [INFO] Task started: Blastn
[2024-01-24 12:37:33,973] [INFO] Running command: blastn -query GCF_010120715.1_ASM1012071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddc83a59-b242-4fad-a3c1-d74e9ecc697b/dqc_reference/reference_markers.fasta -out GCF_010120715.1_ASM1012071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:34,564] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:34,568] [INFO] Selected 15 target genomes.
[2024-01-24 12:37:34,569] [INFO] Target genome list was writen to GCF_010120715.1_ASM1012071v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:34,577] [INFO] Task started: fastANI
[2024-01-24 12:37:34,578] [INFO] Running command: fastANI --query /var/lib/cwl/stg49414d62-f238-46c4-8541-a50cd5d257f5/GCF_010120715.1_ASM1012071v1_genomic.fna.gz --refList GCF_010120715.1_ASM1012071v1_genomic.fna/target_genomes.txt --output GCF_010120715.1_ASM1012071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:43,691] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:43,692] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgddc83a59-b242-4fad-a3c1-d74e9ecc697b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:43,693] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgddc83a59-b242-4fad-a3c1-d74e9ecc697b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:43,701] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:43,701] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:43,701] [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
Aminipila terrae	strain=CBA3637	GCA_010120715.1	2697030	2697030	type	True	100.0	1170	1170	95	conclusive
Aminipila luticellarii	strain=JN-18	GCA_004103735.1	2507160	2507160	type	True	80.3207	443	1170	95	below_threshold
Aminipila butyrica	strain=DSM 103574	GCA_010669305.1	433296	433296	type	True	79.3164	249	1170	95	below_threshold
Anaerovorax odorimutans	strain=DSM 5092	GCA_000426305.1	109327	109327	type	True	77.2863	78	1170	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:43,704] [INFO] DFAST Taxonomy check result was written to GCF_010120715.1_ASM1012071v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:43,705] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:43,705] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:43,705] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgddc83a59-b242-4fad-a3c1-d74e9ecc697b/dqc_reference/checkm_data
[2024-01-24 12:37:43,706] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:43,744] [INFO] Task started: CheckM
[2024-01-24 12:37:43,745] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_010120715.1_ASM1012071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_010120715.1_ASM1012071v1_genomic.fna/checkm_input GCF_010120715.1_ASM1012071v1_genomic.fna/checkm_result
[2024-01-24 12:38:11,722] [INFO] Task succeeded: CheckM
[2024-01-24 12:38:11,723] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:38:11,745] [INFO] ===== Completeness check finished =====
[2024-01-24 12:38:11,746] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:38:11,746] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_010120715.1_ASM1012071v1_genomic.fna/markers.fasta)
[2024-01-24 12:38:11,747] [INFO] Task started: Blastn
[2024-01-24 12:38:11,747] [INFO] Running command: blastn -query GCF_010120715.1_ASM1012071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgddc83a59-b242-4fad-a3c1-d74e9ecc697b/dqc_reference/reference_markers_gtdb.fasta -out GCF_010120715.1_ASM1012071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:38:12,572] [INFO] Task succeeded: Blastn
[2024-01-24 12:38:12,577] [INFO] Selected 12 target genomes.
[2024-01-24 12:38:12,577] [INFO] Target genome list was writen to GCF_010120715.1_ASM1012071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:38:12,595] [INFO] Task started: fastANI
[2024-01-24 12:38:12,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg49414d62-f238-46c4-8541-a50cd5d257f5/GCF_010120715.1_ASM1012071v1_genomic.fna.gz --refList GCF_010120715.1_ASM1012071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_010120715.1_ASM1012071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:18,595] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:18,600] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:18,601] [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_010120715.1	s__Aminipila terrae	100.0	1169	1170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004103735.1	s__Aminipila sp004103735	80.3481	444	1170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002455605.1	s__Aminipila sp002455605	79.5027	357	1170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	99.31	99.31	0.92	0.92	2	-
GCF_010669305.1	s__Aminipila butyrica	79.2955	248	1170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017255415.1	s__Aminipila aminobutyricum	78.1235	168	1170	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__Aminipila	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:18,602] [INFO] GTDB search result was written to GCF_010120715.1_ASM1012071v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:18,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:18,605] [INFO] DFAST_QC result json was written to GCF_010120715.1_ASM1012071v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:18,605] [INFO] DFAST_QC completed!
[2024-01-24 12:38:18,606] [INFO] Total running time: 0h0m54s