[2023-06-05 18:57:44,126] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:57:44,128] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:57:44,128] [INFO] DQC Reference Directory: /var/lib/cwl/stgf8f69c62-8602-4cdc-81a0-abb1f2a4af44/dqc_reference
[2023-06-05 18:57:45,230] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:57:45,231] [INFO] Task started: Prodigal
[2023-06-05 18:57:45,231] [INFO] Running command: gunzip -c /var/lib/cwl/stg3d449d3b-a872-4f90-95c0-04eee4f774c5/GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna.gz | prodigal -d GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/cds.fna -a GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:57:46,332] [INFO] Task succeeded: Prodigal
[2023-06-05 18:57:46,332] [INFO] Task started: HMMsearch
[2023-06-05 18:57:46,332] [INFO] Running command: hmmsearch --tblout GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf8f69c62-8602-4cdc-81a0-abb1f2a4af44/dqc_reference/reference_markers.hmm GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:57:46,500] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:57:46,501] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg3d449d3b-a872-4f90-95c0-04eee4f774c5/GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna.gz]
[2023-06-05 18:57:46,514] [INFO] Query marker FASTA was written to GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/markers.fasta
[2023-06-05 18:57:46,514] [INFO] Task started: Blastn
[2023-06-05 18:57:46,514] [INFO] Running command: blastn -query GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8f69c62-8602-4cdc-81a0-abb1f2a4af44/dqc_reference/reference_markers.fasta -out GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:57:47,039] [INFO] Task succeeded: Blastn
[2023-06-05 18:57:47,043] [INFO] Selected 26 target genomes.
[2023-06-05 18:57:47,043] [INFO] Target genome list was writen to GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/target_genomes.txt
[2023-06-05 18:57:47,048] [INFO] Task started: fastANI
[2023-06-05 18:57:47,048] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d449d3b-a872-4f90-95c0-04eee4f774c5/GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna.gz --refList GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/target_genomes.txt --output GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:57:58,462] [INFO] Task succeeded: fastANI
[2023-06-05 18:57:58,463] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf8f69c62-8602-4cdc-81a0-abb1f2a4af44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:57:58,463] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf8f69c62-8602-4cdc-81a0-abb1f2a4af44/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:57:58,464] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:57:58,464] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 18:57:58,464] [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
--------------------------------------------------------------------------------
[2023-06-05 18:57:58,467] [INFO] DFAST Taxonomy check result was written to GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/tc_result.tsv
[2023-06-05 18:57:58,467] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:57:58,467] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:57:58,467] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf8f69c62-8602-4cdc-81a0-abb1f2a4af44/dqc_reference/checkm_data
[2023-06-05 18:57:58,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:57:58,481] [INFO] Task started: CheckM
[2023-06-05 18:57:58,481] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/checkm_input GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/checkm_result
[2023-06-05 18:58:08,857] [INFO] Task succeeded: CheckM
[2023-06-05 18:58:08,858] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:58:08,873] [INFO] ===== Completeness check finished =====
[2023-06-05 18:58:08,873] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:58:08,873] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/markers.fasta)
[2023-06-05 18:58:08,874] [INFO] Task started: Blastn
[2023-06-05 18:58:08,874] [INFO] Running command: blastn -query GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/markers.fasta -db /var/lib/cwl/stgf8f69c62-8602-4cdc-81a0-abb1f2a4af44/dqc_reference/reference_markers_gtdb.fasta -out GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:58:09,646] [INFO] Task succeeded: Blastn
[2023-06-05 18:58:09,649] [INFO] Selected 20 target genomes.
[2023-06-05 18:58:09,650] [INFO] Target genome list was writen to GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:58:09,661] [INFO] Task started: fastANI
[2023-06-05 18:58:09,661] [INFO] Running command: fastANI --query /var/lib/cwl/stg3d449d3b-a872-4f90-95c0-04eee4f774c5/GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna.gz --refList GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/target_genomes_gtdb.txt --output GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:58:13,790] [INFO] Task succeeded: fastANI
[2023-06-05 18:58:13,796] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:58:13,796] [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_900321795.1	s__RUG727 sp900321795	100.0	239	241	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG727	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCA_902797005.1	s__RUG727 sp902797005	83.0338	141	241	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG727	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016292035.1	s__RUG727 sp016292035	77.4142	74	241	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__RUG727	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000438415.1	s__CAG-628 sp000438415	77.2929	72	241	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628	95.0	97.86	97.71	0.86	0.83	4	-
GCA_003524085.1	s__CAG-628 sp003524085	77.2107	63	241	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628	95.0	98.02	97.61	0.90	0.89	5	-
GCA_900553835.1	s__CAG-628 sp900553835	77.0233	54	241	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__CAG-628	95.0	99.81	99.81	0.82	0.82	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:58:13,797] [INFO] GTDB search result was written to GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/result_gtdb.tsv
[2023-06-05 18:58:13,798] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:58:13,800] [INFO] DFAST_QC result json was written to GCA_902759575.1_Rumen_uncultured_genome_RUG10480_genomic.fna/dqc_result.json
[2023-06-05 18:58:13,800] [INFO] DFAST_QC completed!
[2023-06-05 18:58:13,800] [INFO] Total running time: 0h0m30s