[2023-06-29 20:02:35,115] [INFO] DFAST_QC pipeline started.
[2023-06-29 20:02:35,119] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 20:02:35,119] [INFO] DQC Reference Directory: /var/lib/cwl/stg958b3801-7869-4e4c-974a-838be28a971d/dqc_reference
[2023-06-29 20:02:36,384] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 20:02:36,385] [INFO] Task started: Prodigal
[2023-06-29 20:02:36,385] [INFO] Running command: gunzip -c /var/lib/cwl/stg181a0781-e31d-4e2d-864f-8c2acb32a966/GCA_023708125.1_ASM2370812v1_genomic.fna.gz | prodigal -d GCA_023708125.1_ASM2370812v1_genomic.fna/cds.fna -a GCA_023708125.1_ASM2370812v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 20:02:41,076] [INFO] Task succeeded: Prodigal
[2023-06-29 20:02:41,076] [INFO] Task started: HMMsearch
[2023-06-29 20:02:41,076] [INFO] Running command: hmmsearch --tblout GCA_023708125.1_ASM2370812v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg958b3801-7869-4e4c-974a-838be28a971d/dqc_reference/reference_markers.hmm GCA_023708125.1_ASM2370812v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 20:02:41,341] [INFO] Task succeeded: HMMsearch
[2023-06-29 20:02:41,342] [INFO] Found 6/6 markers.
[2023-06-29 20:02:41,365] [INFO] Query marker FASTA was written to GCA_023708125.1_ASM2370812v1_genomic.fna/markers.fasta
[2023-06-29 20:02:41,366] [INFO] Task started: Blastn
[2023-06-29 20:02:41,366] [INFO] Running command: blastn -query GCA_023708125.1_ASM2370812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg958b3801-7869-4e4c-974a-838be28a971d/dqc_reference/reference_markers.fasta -out GCA_023708125.1_ASM2370812v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:02:42,043] [INFO] Task succeeded: Blastn
[2023-06-29 20:02:42,051] [INFO] Selected 28 target genomes.
[2023-06-29 20:02:42,051] [INFO] Target genome list was writen to GCA_023708125.1_ASM2370812v1_genomic.fna/target_genomes.txt
[2023-06-29 20:02:42,053] [INFO] Task started: fastANI
[2023-06-29 20:02:42,054] [INFO] Running command: fastANI --query /var/lib/cwl/stg181a0781-e31d-4e2d-864f-8c2acb32a966/GCA_023708125.1_ASM2370812v1_genomic.fna.gz --refList GCA_023708125.1_ASM2370812v1_genomic.fna/target_genomes.txt --output GCA_023708125.1_ASM2370812v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 20:03:06,376] [INFO] Task succeeded: fastANI
[2023-06-29 20:03:06,376] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg958b3801-7869-4e4c-974a-838be28a971d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 20:03:06,377] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg958b3801-7869-4e4c-974a-838be28a971d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 20:03:06,382] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 20:03:06,382] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-29 20:03:06,382] [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	90.4222	496	596	95	below_threshold
Turicimonas muris	strain=YL45	GCA_002221595.1	1796652	1796652	type	True	77.4297	104	596	95	below_threshold
Turicimonas muris	strain=YL45	GCA_016696765.1	1796652	1796652	type	True	77.3823	102	596	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-29 20:03:06,385] [INFO] DFAST Taxonomy check result was written to GCA_023708125.1_ASM2370812v1_genomic.fna/tc_result.tsv
[2023-06-29 20:03:06,385] [INFO] ===== Taxonomy check completed =====
[2023-06-29 20:03:06,386] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 20:03:06,386] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg958b3801-7869-4e4c-974a-838be28a971d/dqc_reference/checkm_data
[2023-06-29 20:03:06,387] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 20:03:06,415] [INFO] Task started: CheckM
[2023-06-29 20:03:06,415] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_023708125.1_ASM2370812v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_023708125.1_ASM2370812v1_genomic.fna/checkm_input GCA_023708125.1_ASM2370812v1_genomic.fna/checkm_result
[2023-06-29 20:03:27,954] [INFO] Task succeeded: CheckM
[2023-06-29 20:03:27,955] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 20:03:27,979] [INFO] ===== Completeness check finished =====
[2023-06-29 20:03:27,980] [INFO] ===== Start GTDB Search =====
[2023-06-29 20:03:27,980] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_023708125.1_ASM2370812v1_genomic.fna/markers.fasta)
[2023-06-29 20:03:27,980] [INFO] Task started: Blastn
[2023-06-29 20:03:27,981] [INFO] Running command: blastn -query GCA_023708125.1_ASM2370812v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg958b3801-7869-4e4c-974a-838be28a971d/dqc_reference/reference_markers_gtdb.fasta -out GCA_023708125.1_ASM2370812v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 20:03:28,919] [INFO] Task succeeded: Blastn
[2023-06-29 20:03:28,924] [INFO] Selected 7 target genomes.
[2023-06-29 20:03:28,924] [INFO] Target genome list was writen to GCA_023708125.1_ASM2370812v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 20:03:28,928] [INFO] Task started: fastANI
[2023-06-29 20:03:28,929] [INFO] Running command: fastANI --query /var/lib/cwl/stg181a0781-e31d-4e2d-864f-8c2acb32a966/GCA_023708125.1_ASM2370812v1_genomic.fna.gz --refList GCA_023708125.1_ASM2370812v1_genomic.fna/target_genomes_gtdb.txt --output GCA_023708125.1_ASM2370812v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 20:03:31,975] [INFO] Task succeeded: fastANI
[2023-06-29 20:03:31,986] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-29 20:03:31,986] [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
GCA_000980495.1	s__Parasutterella gallistercoris	99.4077	503	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	99.26	98.76	0.91	0.84	9	conclusive
GCA_900766055.1	s__Parasutterella sp900766055	93.4762	466	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	99.97	99.97	0.95	0.95	2	-
GCA_900552195.1	s__Parasutterella sp900552195	91.988	278	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	98.66	98.32	0.88	0.67	7	-
GCF_000205025.1	s__Parasutterella excrementihominis	90.438	495	596	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__Parasutterella	95.0	98.19	97.92	0.84	0.81	25	-
GCA_900554375.1	s__Parasutterella sp900554375	85.2887	252	596	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	78.6967	175	596	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 20:03:31,988] [INFO] GTDB search result was written to GCA_023708125.1_ASM2370812v1_genomic.fna/result_gtdb.tsv
[2023-06-29 20:03:31,989] [INFO] ===== GTDB Search completed =====
[2023-06-29 20:03:32,005] [INFO] DFAST_QC result json was written to GCA_023708125.1_ASM2370812v1_genomic.fna/dqc_result.json
[2023-06-29 20:03:32,006] [INFO] DFAST_QC completed!
[2023-06-29 20:03:32,006] [INFO] Total running time: 0h0m57s