[2023-06-13 04:47:15,078] [INFO] DFAST_QC pipeline started.
[2023-06-13 04:47:15,080] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 04:47:15,081] [INFO] DQC Reference Directory: /var/lib/cwl/stg9851638d-2ec2-4369-960d-1cae8e9876c5/dqc_reference
[2023-06-13 04:47:16,270] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 04:47:16,271] [INFO] Task started: Prodigal
[2023-06-13 04:47:16,271] [INFO] Running command: gunzip -c /var/lib/cwl/stg5cedbd32-649e-4298-920e-e95ffdf88218/GCA_022483485.1_ASM2248348v1_genomic.fna.gz | prodigal -d GCA_022483485.1_ASM2248348v1_genomic.fna/cds.fna -a GCA_022483485.1_ASM2248348v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 04:47:24,726] [INFO] Task succeeded: Prodigal
[2023-06-13 04:47:24,727] [INFO] Task started: HMMsearch
[2023-06-13 04:47:24,727] [INFO] Running command: hmmsearch --tblout GCA_022483485.1_ASM2248348v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9851638d-2ec2-4369-960d-1cae8e9876c5/dqc_reference/reference_markers.hmm GCA_022483485.1_ASM2248348v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 04:47:24,980] [INFO] Task succeeded: HMMsearch
[2023-06-13 04:47:24,983] [INFO] Found 6/6 markers.
[2023-06-13 04:47:25,011] [INFO] Query marker FASTA was written to GCA_022483485.1_ASM2248348v1_genomic.fna/markers.fasta
[2023-06-13 04:47:25,011] [INFO] Task started: Blastn
[2023-06-13 04:47:25,012] [INFO] Running command: blastn -query GCA_022483485.1_ASM2248348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9851638d-2ec2-4369-960d-1cae8e9876c5/dqc_reference/reference_markers.fasta -out GCA_022483485.1_ASM2248348v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:47:25,651] [INFO] Task succeeded: Blastn
[2023-06-13 04:47:25,656] [INFO] Selected 22 target genomes.
[2023-06-13 04:47:25,656] [INFO] Target genome list was writen to GCA_022483485.1_ASM2248348v1_genomic.fna/target_genomes.txt
[2023-06-13 04:47:25,659] [INFO] Task started: fastANI
[2023-06-13 04:47:25,659] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cedbd32-649e-4298-920e-e95ffdf88218/GCA_022483485.1_ASM2248348v1_genomic.fna.gz --refList GCA_022483485.1_ASM2248348v1_genomic.fna/target_genomes.txt --output GCA_022483485.1_ASM2248348v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 04:47:38,289] [INFO] Task succeeded: fastANI
[2023-06-13 04:47:38,289] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9851638d-2ec2-4369-960d-1cae8e9876c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 04:47:38,290] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9851638d-2ec2-4369-960d-1cae8e9876c5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 04:47:38,297] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 04:47:38,298] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-13 04:47:38,298] [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
Clostridium vitabionis	strain=YH-T4B42	GCA_015351765.1	2784388	2784388	type	True	80.0146	68	1031	95	below_threshold
Porcincola intestinalis	strain=Oil+RF-744-WCA-WT-11	GCA_009696445.1	2606632	2606632	type	True	79.7352	60	1031	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-13 04:47:38,300] [INFO] DFAST Taxonomy check result was written to GCA_022483485.1_ASM2248348v1_genomic.fna/tc_result.tsv
[2023-06-13 04:47:38,300] [INFO] ===== Taxonomy check completed =====
[2023-06-13 04:47:38,300] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 04:47:38,301] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9851638d-2ec2-4369-960d-1cae8e9876c5/dqc_reference/checkm_data
[2023-06-13 04:47:38,302] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 04:47:38,338] [INFO] Task started: CheckM
[2023-06-13 04:47:38,338] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022483485.1_ASM2248348v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022483485.1_ASM2248348v1_genomic.fna/checkm_input GCA_022483485.1_ASM2248348v1_genomic.fna/checkm_result
[2023-06-13 04:48:08,536] [INFO] Task succeeded: CheckM
[2023-06-13 04:48:08,538] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-13 04:48:08,563] [INFO] ===== Completeness check finished =====
[2023-06-13 04:48:08,563] [INFO] ===== Start GTDB Search =====
[2023-06-13 04:48:08,564] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022483485.1_ASM2248348v1_genomic.fna/markers.fasta)
[2023-06-13 04:48:08,564] [INFO] Task started: Blastn
[2023-06-13 04:48:08,564] [INFO] Running command: blastn -query GCA_022483485.1_ASM2248348v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9851638d-2ec2-4369-960d-1cae8e9876c5/dqc_reference/reference_markers_gtdb.fasta -out GCA_022483485.1_ASM2248348v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 04:48:09,653] [INFO] Task succeeded: Blastn
[2023-06-13 04:48:09,660] [INFO] Selected 28 target genomes.
[2023-06-13 04:48:09,660] [INFO] Target genome list was writen to GCA_022483485.1_ASM2248348v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 04:48:09,670] [INFO] Task started: fastANI
[2023-06-13 04:48:09,670] [INFO] Running command: fastANI --query /var/lib/cwl/stg5cedbd32-649e-4298-920e-e95ffdf88218/GCA_022483485.1_ASM2248348v1_genomic.fna.gz --refList GCA_022483485.1_ASM2248348v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022483485.1_ASM2248348v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 04:48:22,837] [INFO] Task succeeded: fastANI
[2023-06-13 04:48:22,850] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 04:48:22,850] [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_900317475.1	s__CAG-791 sp900317475	98.7153	611	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.34	98.93	0.86	0.78	29	conclusive
GCA_000431495.1	s__CAG-791 sp000431495	78.7073	86	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.54	97.54	0.90	0.90	2	-
GCA_900320025.1	s__CAG-791 sp900320025	78.3268	166	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.86	98.12	0.80	0.73	19	-
GCA_902781655.1	s__CAG-791 sp902781655	78.2357	193	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900315055.1	s__CAG-791 sp900315055	77.292	123	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.03	98.45	0.88	0.84	8	-
GCF_900625025.1	s__CAG-791 sp900625025	77.0267	106	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432565.1	s__CAG-791 sp017432565	76.7326	67	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900107575.1	s__CAG-791 sp900107575	76.5962	82	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449485.1	s__CAG-791 sp017449485	76.4798	57	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.27	96.27	0.75	0.75	2	-
GCA_902781215.1	s__CAG-791 sp902781215	76.3493	58	1031	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	96.36	96.36	0.81	0.81	2	-
--------------------------------------------------------------------------------
[2023-06-13 04:48:22,853] [INFO] GTDB search result was written to GCA_022483485.1_ASM2248348v1_genomic.fna/result_gtdb.tsv
[2023-06-13 04:48:22,853] [INFO] ===== GTDB Search completed =====
[2023-06-13 04:48:22,856] [INFO] DFAST_QC result json was written to GCA_022483485.1_ASM2248348v1_genomic.fna/dqc_result.json
[2023-06-13 04:48:22,856] [INFO] DFAST_QC completed!
[2023-06-13 04:48:22,856] [INFO] Total running time: 0h1m8s