[2023-06-29 12:40:58,728] [INFO] DFAST_QC pipeline started.
[2023-06-29 12:40:58,731] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 12:40:58,731] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2a0c8ff-f1e3-483e-b80e-8a46e77ba9c9/dqc_reference
[2023-06-29 12:40:59,969] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 12:40:59,970] [INFO] Task started: Prodigal
[2023-06-29 12:40:59,971] [INFO] Running command: gunzip -c /var/lib/cwl/stg4cd84395-915f-408c-a093-b949a5a43b40/GCA_023708425.1_ASM2370842v1_genomic.fna.gz | prodigal -d GCA_023708425.1_ASM2370842v1_genomic.fna/cds.fna -a GCA_023708425.1_ASM2370842v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 12:41:06,179] [INFO] Task succeeded: Prodigal
[2023-06-29 12:41:06,179] [INFO] Task started: HMMsearch
[2023-06-29 12:41:06,179] [INFO] Running command: hmmsearch --tblout GCA_023708425.1_ASM2370842v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2a0c8ff-f1e3-483e-b80e-8a46e77ba9c9/dqc_reference/reference_markers.hmm GCA_023708425.1_ASM2370842v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 12:41:06,446] [INFO] Task succeeded: HMMsearch
[2023-06-29 12:41:06,447] [INFO] Found 6/6 markers.
[2023-06-29 12:41:06,476] [INFO] Query marker FASTA was written to GCA_023708425.1_ASM2370842v1_genomic.fna/markers.fasta
[2023-06-29 12:41:06,477] [INFO] Task started: Blastn
[2023-06-29 12:41:06,477] [INFO] Running command: blastn -query GCA_023708425.1_ASM2370842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2a0c8ff-f1e3-483e-b80e-8a46e77ba9c9/dqc_reference/reference_markers.fasta -out GCA_023708425.1_ASM2370842v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:07,105] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:07,111] [INFO] Selected 28 target genomes.
[2023-06-29 12:41:07,111] [INFO] Target genome list was writen to GCA_023708425.1_ASM2370842v1_genomic.fna/target_genomes.txt
[2023-06-29 12:41:07,123] [INFO] Task started: fastANI
[2023-06-29 12:41:07,123] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cd84395-915f-408c-a093-b949a5a43b40/GCA_023708425.1_ASM2370842v1_genomic.fna.gz --refList GCA_023708425.1_ASM2370842v1_genomic.fna/target_genomes.txt --output GCA_023708425.1_ASM2370842v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 12:41:23,360] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:23,361] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2a0c8ff-f1e3-483e-b80e-8a46e77ba9c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 12:41:23,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2a0c8ff-f1e3-483e-b80e-8a46e77ba9c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 12:41:23,369] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2023-06-29 12:41:23,369] [INFO] The taxonomy check result is classified as 'conclusive'.
[2023-06-29 12:41:23,369] [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
Parasutterella excrementihominis	strain=YIT 11859	GCA_000205025.1	487175	487175	type	True	98.7406	716	845	95	conclusive
Turicimonas muris	strain=YL45	GCA_016696765.1	1796652	1796652	type	True	78.018	118	845	95	below_threshold
Turicimonas muris	strain=YL45	GCA_002221595.1	1796652	1796652	type	True	77.9327	117	845	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 12:41:23,371] [INFO] DFAST Taxonomy check result was written to GCA_023708425.1_ASM2370842v1_genomic.fna/tc_result.tsv
[2023-06-29 12:41:23,372] [INFO] ===== Taxonomy check completed =====
[2023-06-29 12:41:23,372] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 12:41:23,372] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2a0c8ff-f1e3-483e-b80e-8a46e77ba9c9/dqc_reference/checkm_data
[2023-06-29 12:41:23,373] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 12:41:23,405] [INFO] Task started: CheckM
[2023-06-29 12:41:23,405] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708425.1_ASM2370842v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708425.1_ASM2370842v1_genomic.fna/checkm_input GCA_023708425.1_ASM2370842v1_genomic.fna/checkm_result
[2023-06-29 12:41:48,413] [INFO] Task succeeded: CheckM
[2023-06-29 12:41:48,414] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 12:41:48,432] [INFO] ===== Completeness check finished =====
[2023-06-29 12:41:48,433] [INFO] ===== Start GTDB Search =====
[2023-06-29 12:41:48,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708425.1_ASM2370842v1_genomic.fna/markers.fasta)
[2023-06-29 12:41:48,434] [INFO] Task started: Blastn
[2023-06-29 12:41:48,434] [INFO] Running command: blastn -query GCA_023708425.1_ASM2370842v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2a0c8ff-f1e3-483e-b80e-8a46e77ba9c9/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708425.1_ASM2370842v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 12:41:49,321] [INFO] Task succeeded: Blastn
[2023-06-29 12:41:49,326] [INFO] Selected 10 target genomes.
[2023-06-29 12:41:49,326] [INFO] Target genome list was writen to GCA_023708425.1_ASM2370842v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 12:41:49,336] [INFO] Task started: fastANI
[2023-06-29 12:41:49,337] [INFO] Running command: fastANI --query /var/lib/cwl/stg4cd84395-915f-408c-a093-b949a5a43b40/GCA_023708425.1_ASM2370842v1_genomic.fna.gz --refList GCA_023708425.1_ASM2370842v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708425.1_ASM2370842v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 12:41:54,509] [INFO] Task succeeded: fastANI
[2023-06-29 12:41:54,519] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 12:41:54,520] [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_000205025.1	s__Parasutterella excrementihominis	98.7875	714	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	98.19	97.92	0.84	0.81	25	conclusive
GCA_900552195.1	s__Parasutterella sp900552195	94.6942	325	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	98.66	98.32	0.88	0.67	7	-
GCA_900766055.1	s__Parasutterella sp900766055	91.4375	611	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	99.97	99.97	0.95	0.95	2	-
GCA_000980495.1	s__Parasutterella gallistercoris	90.2983	582	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	99.26	98.76	0.91	0.84	9	-
GCA_900554375.1	s__Parasutterella sp900554375	86.8782	323	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009767915.1	s__Parasutterella sp009767915	78.5619	203	845	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	98.92	98.38	0.92	0.85	5	-
--------------------------------------------------------------------------------
[2023-06-29 12:41:54,522] [INFO] GTDB search result was written to GCA_023708425.1_ASM2370842v1_genomic.fna/result_gtdb.tsv
[2023-06-29 12:41:54,522] [INFO] ===== GTDB Search completed =====
[2023-06-29 12:41:54,525] [INFO] DFAST_QC result json was written to GCA_023708425.1_ASM2370842v1_genomic.fna/dqc_result.json
[2023-06-29 12:41:54,525] [INFO] DFAST_QC completed!
[2023-06-29 12:41:54,525] [INFO] Total running time: 0h0m56s