[2023-06-07 22:55:03,900] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:55:03,902] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:55:03,903] [INFO] DQC Reference Directory: /var/lib/cwl/stg6bb43bc1-225f-44bd-8bf0-c4ef5412b5dc/dqc_reference
[2023-06-07 22:55:05,167] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:55:05,167] [INFO] Task started: Prodigal
[2023-06-07 22:55:05,168] [INFO] Running command: gunzip -c /var/lib/cwl/stg8607dd42-4ea6-4de3-a40c-8e365533b9c3/GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna.gz | prodigal -d GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/cds.fna -a GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:55:11,456] [INFO] Task succeeded: Prodigal
[2023-06-07 22:55:11,457] [INFO] Task started: HMMsearch
[2023-06-07 22:55:11,457] [INFO] Running command: hmmsearch --tblout GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6bb43bc1-225f-44bd-8bf0-c4ef5412b5dc/dqc_reference/reference_markers.hmm GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:55:11,686] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:55:11,687] [INFO] Found 6/6 markers.
[2023-06-07 22:55:11,712] [INFO] Query marker FASTA was written to GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/markers.fasta
[2023-06-07 22:55:11,712] [INFO] Task started: Blastn
[2023-06-07 22:55:11,712] [INFO] Running command: blastn -query GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bb43bc1-225f-44bd-8bf0-c4ef5412b5dc/dqc_reference/reference_markers.fasta -out GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:12,364] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:12,368] [INFO] Selected 26 target genomes.
[2023-06-07 22:55:12,369] [INFO] Target genome list was writen to GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/target_genomes.txt
[2023-06-07 22:55:12,370] [INFO] Task started: fastANI
[2023-06-07 22:55:12,370] [INFO] Running command: fastANI --query /var/lib/cwl/stg8607dd42-4ea6-4de3-a40c-8e365533b9c3/GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna.gz --refList GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/target_genomes.txt --output GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:55:27,827] [INFO] Task succeeded: fastANI
[2023-06-07 22:55:27,828] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6bb43bc1-225f-44bd-8bf0-c4ef5412b5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:55:27,829] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6bb43bc1-225f-44bd-8bf0-c4ef5412b5dc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:55:27,834] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:55:27,834] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:55:27,834] [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	76.9077	56	704	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:55:27,837] [INFO] DFAST Taxonomy check result was written to GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/tc_result.tsv
[2023-06-07 22:55:27,837] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:55:27,838] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:55:27,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6bb43bc1-225f-44bd-8bf0-c4ef5412b5dc/dqc_reference/checkm_data
[2023-06-07 22:55:27,840] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:55:27,872] [INFO] Task started: CheckM
[2023-06-07 22:55:27,873] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/checkm_input GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/checkm_result
[2023-06-07 22:55:52,215] [INFO] Task succeeded: CheckM
[2023-06-07 22:55:52,217] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 22:55:52,238] [INFO] ===== Completeness check finished =====
[2023-06-07 22:55:52,239] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:55:52,239] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/markers.fasta)
[2023-06-07 22:55:52,240] [INFO] Task started: Blastn
[2023-06-07 22:55:52,240] [INFO] Running command: blastn -query GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/markers.fasta -db /var/lib/cwl/stg6bb43bc1-225f-44bd-8bf0-c4ef5412b5dc/dqc_reference/reference_markers_gtdb.fasta -out GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:53,284] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:53,288] [INFO] Selected 21 target genomes.
[2023-06-07 22:55:53,288] [INFO] Target genome list was writen to GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:55:53,290] [INFO] Task started: fastANI
[2023-06-07 22:55:53,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg8607dd42-4ea6-4de3-a40c-8e365533b9c3/GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna.gz --refList GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/target_genomes_gtdb.txt --output GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:56:01,953] [INFO] Task succeeded: fastANI
[2023-06-07 22:56:01,976] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:56:01,976] [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_900318875.1	s__CAG-791 sp900318875	99.3146	631	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.20	98.52	0.87	0.80	24	conclusive
GCA_002353635.1	s__CAG-791 sp002353635	79.346	114	704	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	78.9871	247	704	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	-
GCA_900107575.1	s__CAG-791 sp900107575	77.5234	151	704	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_900316855.1	s__CAG-791 sp900316855	77.3465	145	704	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.99	99.99	0.99	0.99	2	-
GCA_000431495.1	s__CAG-791 sp000431495	77.3228	96	704	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_002372815.1	s__CAG-791 sp002372815	77.0149	70	704	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_902781655.1	s__CAG-791 sp902781655	76.9561	81	704	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_017449745.1	s__CAG-791 sp017449745	76.9167	80	704	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_002395235.1	s__CAG-791 sp002395235	76.8875	61	704	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_902781215.1	s__CAG-791 sp902781215	76.7766	102	704	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	-
GCA_902796425.1	s__CAG-791 sp902796425	76.3071	73	704	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	-
--------------------------------------------------------------------------------
[2023-06-07 22:56:01,978] [INFO] GTDB search result was written to GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/result_gtdb.tsv
[2023-06-07 22:56:01,979] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:56:01,982] [INFO] DFAST_QC result json was written to GCA_902786185.1_Rumen_uncultured_genome_RUG13145_genomic.fna/dqc_result.json
[2023-06-07 22:56:01,982] [INFO] DFAST_QC completed!
[2023-06-07 22:56:01,982] [INFO] Total running time: 0h0m58s