[2024-01-24 12:31:56,107] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:56,109] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:56,109] [INFO] DQC Reference Directory: /var/lib/cwl/stgefef0632-defb-4367-ae6b-ff09386990c1/dqc_reference
[2024-01-24 12:31:57,398] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:57,398] [INFO] Task started: Prodigal
[2024-01-24 12:31:57,399] [INFO] Running command: gunzip -c /var/lib/cwl/stgb794b786-feaf-4f35-bd0e-55ff27c5349b/GCF_007827295.1_ASM782729v1_genomic.fna.gz | prodigal -d GCF_007827295.1_ASM782729v1_genomic.fna/cds.fna -a GCF_007827295.1_ASM782729v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:32:04,974] [INFO] Task succeeded: Prodigal
[2024-01-24 12:32:04,974] [INFO] Task started: HMMsearch
[2024-01-24 12:32:04,975] [INFO] Running command: hmmsearch --tblout GCF_007827295.1_ASM782729v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgefef0632-defb-4367-ae6b-ff09386990c1/dqc_reference/reference_markers.hmm GCF_007827295.1_ASM782729v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:32:05,222] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:32:05,223] [INFO] Found 6/6 markers.
[2024-01-24 12:32:05,248] [INFO] Query marker FASTA was written to GCF_007827295.1_ASM782729v1_genomic.fna/markers.fasta
[2024-01-24 12:32:05,248] [INFO] Task started: Blastn
[2024-01-24 12:32:05,248] [INFO] Running command: blastn -query GCF_007827295.1_ASM782729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefef0632-defb-4367-ae6b-ff09386990c1/dqc_reference/reference_markers.fasta -out GCF_007827295.1_ASM782729v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:05,831] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:05,837] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:05,837] [INFO] Target genome list was writen to GCF_007827295.1_ASM782729v1_genomic.fna/target_genomes.txt
[2024-01-24 12:32:05,863] [INFO] Task started: fastANI
[2024-01-24 12:32:05,864] [INFO] Running command: fastANI --query /var/lib/cwl/stgb794b786-feaf-4f35-bd0e-55ff27c5349b/GCF_007827295.1_ASM782729v1_genomic.fna.gz --refList GCF_007827295.1_ASM782729v1_genomic.fna/target_genomes.txt --output GCF_007827295.1_ASM782729v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:32:18,151] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:18,151] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgefef0632-defb-4367-ae6b-ff09386990c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:32:18,152] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgefef0632-defb-4367-ae6b-ff09386990c1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:32:18,156] [INFO] Found 3 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:32:18,156] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:32:18,156] [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
Seleniivibrio woodruffii	strain=S4	GCA_007827295.1	1078050	1078050	type	True	100.0	973	975	95	conclusive
Seleniivibrio woodruffii	strain=DSM 24984	GCA_004339245.1	1078050	1078050	type	True	99.9857	964	975	95	conclusive
Denitrovibrio acetiphilus	strain=DSM 12809	GCA_000025725.1	118000	118000	type	True	76.9235	83	975	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:32:18,158] [INFO] DFAST Taxonomy check result was written to GCF_007827295.1_ASM782729v1_genomic.fna/tc_result.tsv
[2024-01-24 12:32:18,159] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:32:18,159] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:32:18,159] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgefef0632-defb-4367-ae6b-ff09386990c1/dqc_reference/checkm_data
[2024-01-24 12:32:18,160] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:32:18,201] [INFO] Task started: CheckM
[2024-01-24 12:32:18,201] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007827295.1_ASM782729v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007827295.1_ASM782729v1_genomic.fna/checkm_input GCF_007827295.1_ASM782729v1_genomic.fna/checkm_result
[2024-01-24 12:32:47,982] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:47,983] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:48,004] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:48,005] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:48,005] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007827295.1_ASM782729v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:48,005] [INFO] Task started: Blastn
[2024-01-24 12:32:48,005] [INFO] Running command: blastn -query GCF_007827295.1_ASM782729v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgefef0632-defb-4367-ae6b-ff09386990c1/dqc_reference/reference_markers_gtdb.fasta -out GCF_007827295.1_ASM782729v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:48,789] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:48,793] [INFO] Selected 16 target genomes.
[2024-01-24 12:32:48,793] [INFO] Target genome list was writen to GCF_007827295.1_ASM782729v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:48,803] [INFO] Task started: fastANI
[2024-01-24 12:32:48,803] [INFO] Running command: fastANI --query /var/lib/cwl/stgb794b786-feaf-4f35-bd0e-55ff27c5349b/GCF_007827295.1_ASM782729v1_genomic.fna.gz --refList GCF_007827295.1_ASM782729v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007827295.1_ASM782729v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:32:59,828] [INFO] Task succeeded: fastANI
[2024-01-24 12:32:59,837] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:32:59,837] [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_004339245.1	s__Seleniivibrio woodruffii	99.9857	964	975	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Seleniivibrio	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCA_002452405.1	s__Seleniivibrio sp002452405	80.4688	558	975	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Seleniivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002452335.1	s__Seleniivibrio sp002452335	78.1139	308	975	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Seleniivibrio	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025725.1	s__Denitrovibrio acetiphilus	76.8162	83	975	d__Bacteria;p__Deferribacterota;c__Deferribacteres;o__Deferribacterales;f__Denitrovibrionaceae;g__Denitrovibrio	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:32:59,839] [INFO] GTDB search result was written to GCF_007827295.1_ASM782729v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:32:59,840] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:32:59,843] [INFO] DFAST_QC result json was written to GCF_007827295.1_ASM782729v1_genomic.fna/dqc_result.json
[2024-01-24 12:32:59,843] [INFO] DFAST_QC completed!
[2024-01-24 12:32:59,843] [INFO] Total running time: 0h1m4s