[2023-06-05 18:05:43,475] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:05:43,490] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:05:43,490] [INFO] DQC Reference Directory: /var/lib/cwl/stgf2f5d9ce-63ad-4474-9d5d-6ab32f1f8263/dqc_reference
[2023-06-05 18:05:44,778] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:05:44,779] [INFO] Task started: Prodigal
[2023-06-05 18:05:44,779] [INFO] Running command: gunzip -c /var/lib/cwl/stg5d4f2afa-3cb5-4050-928e-d6646738effd/GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna.gz | prodigal -d GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/cds.fna -a GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:05:50,710] [INFO] Task succeeded: Prodigal
[2023-06-05 18:05:50,711] [INFO] Task started: HMMsearch
[2023-06-05 18:05:50,711] [INFO] Running command: hmmsearch --tblout GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf2f5d9ce-63ad-4474-9d5d-6ab32f1f8263/dqc_reference/reference_markers.hmm GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:05:50,937] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:05:50,939] [INFO] Found 6/6 markers.
[2023-06-05 18:05:50,974] [INFO] Query marker FASTA was written to GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/markers.fasta
[2023-06-05 18:05:50,975] [INFO] Task started: Blastn
[2023-06-05 18:05:50,975] [INFO] Running command: blastn -query GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2f5d9ce-63ad-4474-9d5d-6ab32f1f8263/dqc_reference/reference_markers.fasta -out GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:05:51,634] [INFO] Task succeeded: Blastn
[2023-06-05 18:05:51,639] [INFO] Selected 28 target genomes.
[2023-06-05 18:05:51,640] [INFO] Target genome list was writen to GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/target_genomes.txt
[2023-06-05 18:05:51,645] [INFO] Task started: fastANI
[2023-06-05 18:05:51,645] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d4f2afa-3cb5-4050-928e-d6646738effd/GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna.gz --refList GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/target_genomes.txt --output GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:06:21,154] [INFO] Task succeeded: fastANI
[2023-06-05 18:06:21,154] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf2f5d9ce-63ad-4474-9d5d-6ab32f1f8263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:06:21,155] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf2f5d9ce-63ad-4474-9d5d-6ab32f1f8263/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:06:21,159] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:06:21,159] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:06:21,159] [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
Bilifractor porci	strain=Oil+RF-744-WCA-WT-13	GCA_009696005.1	2606636	2606636	type	True	76.7785	122	766	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:06:21,161] [INFO] DFAST Taxonomy check result was written to GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/tc_result.tsv
[2023-06-05 18:06:21,167] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:06:21,167] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:06:21,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf2f5d9ce-63ad-4474-9d5d-6ab32f1f8263/dqc_reference/checkm_data
[2023-06-05 18:06:21,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:06:21,237] [INFO] Task started: CheckM
[2023-06-05 18:06:21,237] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/checkm_input GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/checkm_result
[2023-06-05 18:06:52,703] [INFO] Task succeeded: CheckM
[2023-06-05 18:06:52,704] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.95%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 18:06:52,722] [INFO] ===== Completeness check finished =====
[2023-06-05 18:06:52,723] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:06:52,724] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/markers.fasta)
[2023-06-05 18:06:52,724] [INFO] Task started: Blastn
[2023-06-05 18:06:52,724] [INFO] Running command: blastn -query GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/markers.fasta -db /var/lib/cwl/stgf2f5d9ce-63ad-4474-9d5d-6ab32f1f8263/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:06:53,807] [INFO] Task succeeded: Blastn
[2023-06-05 18:06:53,815] [INFO] Selected 16 target genomes.
[2023-06-05 18:06:53,815] [INFO] Target genome list was writen to GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:06:53,828] [INFO] Task started: fastANI
[2023-06-05 18:06:53,828] [INFO] Running command: fastANI --query /var/lib/cwl/stg5d4f2afa-3cb5-4050-928e-d6646738effd/GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna.gz --refList GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/target_genomes_gtdb.txt --output GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:07:02,494] [INFO] Task succeeded: fastANI
[2023-06-05 18:07:02,505] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:07:02,505] [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_900314295.1	s__Bilifractor sp900314295	99.3264	670	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.31	99.31	0.88	0.88	2	conclusive
GCA_903789595.1	s__Bilifractor sp903789595	84.8447	626	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394235.1	s__Bilifractor sp002394235	82.859	517	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.06	98.97	0.80	0.76	4	-
GCA_900770225.1	s__Bilifractor sp900770225	77.0962	119	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318405.1	s__Bilifractor sp900318405	76.951	113	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.33	99.23	0.95	0.94	3	-
GCF_009696005.1	s__Bilifractor porci	76.7788	120	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	98.26	98.26	0.83	0.83	2	-
GCF_000183525.2	s__Bilifractor cellulosolvens	76.6574	100	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902756775.1	s__Bilifractor sp900317175	76.552	101	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	97.95	96.99	0.76	0.63	20	-
GCA_002368795.1	s__Bilifractor sp002368795	76.4956	73	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797025.1	s__Bilifractor sp902797025	76.2578	62	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318755.1	s__Bilifractor sp900318755	76.1696	57	766	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__Bilifractor	95.0	99.38	99.38	0.90	0.90	2	-
--------------------------------------------------------------------------------
[2023-06-05 18:07:02,534] [INFO] GTDB search result was written to GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/result_gtdb.tsv
[2023-06-05 18:07:02,534] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:07:02,539] [INFO] DFAST_QC result json was written to GCA_902797335.1_Rumen_uncultured_genome_RUG14260_genomic.fna/dqc_result.json
[2023-06-05 18:07:02,539] [INFO] DFAST_QC completed!
[2023-06-05 18:07:02,539] [INFO] Total running time: 0h1m19s