[2023-06-08 15:58:25,851] [INFO] DFAST_QC pipeline started.
[2023-06-08 15:58:25,868] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 15:58:25,868] [INFO] DQC Reference Directory: /var/lib/cwl/stgc87b15fc-48ca-435c-a127-d61d5f5a61c6/dqc_reference
[2023-06-08 15:58:27,971] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 15:58:27,972] [INFO] Task started: Prodigal
[2023-06-08 15:58:27,972] [INFO] Running command: gunzip -c /var/lib/cwl/stg649bea36-15b0-42e9-bac7-f80fa9a617ba/GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna.gz | prodigal -d GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/cds.fna -a GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 15:58:34,104] [INFO] Task succeeded: Prodigal
[2023-06-08 15:58:34,104] [INFO] Task started: HMMsearch
[2023-06-08 15:58:34,104] [INFO] Running command: hmmsearch --tblout GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc87b15fc-48ca-435c-a127-d61d5f5a61c6/dqc_reference/reference_markers.hmm GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/protein.faa > /dev/null
[2023-06-08 15:58:34,321] [INFO] Task succeeded: HMMsearch
[2023-06-08 15:58:34,323] [INFO] Found 6/6 markers.
[2023-06-08 15:58:34,350] [INFO] Query marker FASTA was written to GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/markers.fasta
[2023-06-08 15:58:34,350] [INFO] Task started: Blastn
[2023-06-08 15:58:34,350] [INFO] Running command: blastn -query GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/markers.fasta -db /var/lib/cwl/stgc87b15fc-48ca-435c-a127-d61d5f5a61c6/dqc_reference/reference_markers.fasta -out GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:58:35,006] [INFO] Task succeeded: Blastn
[2023-06-08 15:58:35,011] [INFO] Selected 29 target genomes.
[2023-06-08 15:58:35,012] [INFO] Target genome list was writen to GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/target_genomes.txt
[2023-06-08 15:58:35,017] [INFO] Task started: fastANI
[2023-06-08 15:58:35,017] [INFO] Running command: fastANI --query /var/lib/cwl/stg649bea36-15b0-42e9-bac7-f80fa9a617ba/GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna.gz --refList GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/target_genomes.txt --output GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 15:58:51,956] [INFO] Task succeeded: fastANI
[2023-06-08 15:58:51,956] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc87b15fc-48ca-435c-a127-d61d5f5a61c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 15:58:51,957] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc87b15fc-48ca-435c-a127-d61d5f5a61c6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 15:58:51,963] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 15:58:51,963] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 15:58:51,963] [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	76.4638	58	712	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 15:58:51,965] [INFO] DFAST Taxonomy check result was written to GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/tc_result.tsv
[2023-06-08 15:58:51,966] [INFO] ===== Taxonomy check completed =====
[2023-06-08 15:58:51,966] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 15:58:51,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc87b15fc-48ca-435c-a127-d61d5f5a61c6/dqc_reference/checkm_data
[2023-06-08 15:58:51,968] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 15:58:51,997] [INFO] Task started: CheckM
[2023-06-08 15:58:51,997] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/checkm_input GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/checkm_result
[2023-06-08 15:59:17,000] [INFO] Task succeeded: CheckM
[2023-06-08 15:59:17,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.42%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 15:59:17,024] [INFO] ===== Completeness check finished =====
[2023-06-08 15:59:17,024] [INFO] ===== Start GTDB Search =====
[2023-06-08 15:59:17,024] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/markers.fasta)
[2023-06-08 15:59:17,025] [INFO] Task started: Blastn
[2023-06-08 15:59:17,025] [INFO] Running command: blastn -query GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/markers.fasta -db /var/lib/cwl/stgc87b15fc-48ca-435c-a127-d61d5f5a61c6/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 15:59:18,086] [INFO] Task succeeded: Blastn
[2023-06-08 15:59:18,091] [INFO] Selected 19 target genomes.
[2023-06-08 15:59:18,091] [INFO] Target genome list was writen to GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 15:59:18,103] [INFO] Task started: fastANI
[2023-06-08 15:59:18,103] [INFO] Running command: fastANI --query /var/lib/cwl/stg649bea36-15b0-42e9-bac7-f80fa9a617ba/GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna.gz --refList GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/target_genomes_gtdb.txt --output GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 15:59:26,696] [INFO] Task succeeded: fastANI
[2023-06-08 15:59:26,707] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 15:59:26,707] [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_900320025.1	s__CAG-791 sp900320025	98.7827	546	712	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	conclusive
GCA_902781655.1	s__CAG-791 sp902781655	91.9396	599	712	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_900317475.1	s__CAG-791 sp900317475	78.5723	171	712	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	-
GCA_900315055.1	s__CAG-791 sp900315055	77.1147	83	712	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	77.1094	104	712	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	76.5867	77	712	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	-
--------------------------------------------------------------------------------
[2023-06-08 15:59:26,709] [INFO] GTDB search result was written to GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/result_gtdb.tsv
[2023-06-08 15:59:26,710] [INFO] ===== GTDB Search completed =====
[2023-06-08 15:59:26,713] [INFO] DFAST_QC result json was written to GCA_902800175.1_Rumen_uncultured_genome_RUG14548_genomic.fna/dqc_result.json
[2023-06-08 15:59:26,713] [INFO] DFAST_QC completed!
[2023-06-08 15:59:26,713] [INFO] Total running time: 0h1m1s