[2023-06-08 08:35:03,111] [INFO] DFAST_QC pipeline started.
[2023-06-08 08:35:03,113] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 08:35:03,114] [INFO] DQC Reference Directory: /var/lib/cwl/stgc2dabb34-4165-491a-99f4-adf153b5fa60/dqc_reference
[2023-06-08 08:35:06,136] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 08:35:06,138] [INFO] Task started: Prodigal
[2023-06-08 08:35:06,138] [INFO] Running command: gunzip -c /var/lib/cwl/stg37927ab4-ca63-4e66-ae45-e2cd72ba5bed/GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna.gz | prodigal -d GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/cds.fna -a GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 08:35:24,022] [INFO] Task succeeded: Prodigal
[2023-06-08 08:35:24,022] [INFO] Task started: HMMsearch
[2023-06-08 08:35:24,022] [INFO] Running command: hmmsearch --tblout GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc2dabb34-4165-491a-99f4-adf153b5fa60/dqc_reference/reference_markers.hmm GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/protein.faa > /dev/null
[2023-06-08 08:35:24,246] [INFO] Task succeeded: HMMsearch
[2023-06-08 08:35:24,248] [INFO] Found 6/6 markers.
[2023-06-08 08:35:24,283] [INFO] Query marker FASTA was written to GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/markers.fasta
[2023-06-08 08:35:24,283] [INFO] Task started: Blastn
[2023-06-08 08:35:24,283] [INFO] Running command: blastn -query GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2dabb34-4165-491a-99f4-adf153b5fa60/dqc_reference/reference_markers.fasta -out GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:35:24,892] [INFO] Task succeeded: Blastn
[2023-06-08 08:35:24,896] [INFO] Selected 35 target genomes.
[2023-06-08 08:35:24,897] [INFO] Target genome list was writen to GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/target_genomes.txt
[2023-06-08 08:35:24,899] [INFO] Task started: fastANI
[2023-06-08 08:35:24,899] [INFO] Running command: fastANI --query /var/lib/cwl/stg37927ab4-ca63-4e66-ae45-e2cd72ba5bed/GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna.gz --refList GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/target_genomes.txt --output GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 08:35:43,163] [INFO] Task succeeded: fastANI
[2023-06-08 08:35:43,164] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc2dabb34-4165-491a-99f4-adf153b5fa60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 08:35:43,164] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc2dabb34-4165-491a-99f4-adf153b5fa60/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 08:35:43,175] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 08:35:43,175] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 08:35:43,176] [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
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	77.7155	138	905	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	77.6352	141	905	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 08:35:43,178] [INFO] DFAST Taxonomy check result was written to GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/tc_result.tsv
[2023-06-08 08:35:43,179] [INFO] ===== Taxonomy check completed =====
[2023-06-08 08:35:43,179] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 08:35:43,179] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc2dabb34-4165-491a-99f4-adf153b5fa60/dqc_reference/checkm_data
[2023-06-08 08:35:43,181] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 08:35:43,216] [INFO] Task started: CheckM
[2023-06-08 08:35:43,217] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/checkm_input GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/checkm_result
[2023-06-08 08:36:35,797] [INFO] Task succeeded: CheckM
[2023-06-08 08:36:35,799] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 78.99%
Contamintation: 1.04%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-08 08:36:35,823] [INFO] ===== Completeness check finished =====
[2023-06-08 08:36:35,823] [INFO] ===== Start GTDB Search =====
[2023-06-08 08:36:35,824] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/markers.fasta)
[2023-06-08 08:36:35,824] [INFO] Task started: Blastn
[2023-06-08 08:36:35,824] [INFO] Running command: blastn -query GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/markers.fasta -db /var/lib/cwl/stgc2dabb34-4165-491a-99f4-adf153b5fa60/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 08:36:36,690] [INFO] Task succeeded: Blastn
[2023-06-08 08:36:36,695] [INFO] Selected 16 target genomes.
[2023-06-08 08:36:36,695] [INFO] Target genome list was writen to GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 08:36:36,697] [INFO] Task started: fastANI
[2023-06-08 08:36:36,698] [INFO] Running command: fastANI --query /var/lib/cwl/stg37927ab4-ca63-4e66-ae45-e2cd72ba5bed/GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna.gz --refList GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/target_genomes_gtdb.txt --output GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 08:36:47,649] [INFO] Task succeeded: fastANI
[2023-06-08 08:36:47,663] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 08:36:47,663] [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_900319525.1	s__Sodaliphilus sp900319525	97.8506	806	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.42	97.68	0.92	0.87	5	conclusive
GCA_900318535.1	s__Sodaliphilus sp900318535	84.7923	665	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.25	96.02	0.89	0.86	17	-
GCA_902793405.1	s__Sodaliphilus sp902793405	84.7611	681	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	96.00	96.00	0.85	0.85	2	-
GCA_902772455.1	s__Sodaliphilus sp902772455	84.466	624	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017449785.1	s__Sodaliphilus sp017449785	83.8027	543	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017453505.1	s__Sodaliphilus sp017453505	83.4345	545	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900320055.1	s__Sodaliphilus sp900320055	83.3177	546	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.84	98.48	0.90	0.87	16	-
GCA_900317325.1	s__Sodaliphilus sp900317325	83.0136	599	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902760865.1	s__Sodaliphilus sp902760865	82.9688	602	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792895.1	s__Sodaliphilus sp902792895	82.7173	611	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557425.1	s__Sodaliphilus sp017557425	82.7043	520	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776955.1	s__Sodaliphilus sp902776955	82.6604	568	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233915.1	s__Sodaliphilus sp905233915	82.6334	547	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318335.1	s__Sodaliphilus sp900318335	82.5944	582	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.51	96.57	0.89	0.87	11	-
GCA_900320245.1	s__Sodaliphilus sp900320245	82.5568	578	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.46	97.77	0.92	0.88	5	-
GCA_902779125.1	s__Sodaliphilus sp902779125	82.2398	566	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.25	97.06	0.87	0.83	3	-
--------------------------------------------------------------------------------
[2023-06-08 08:36:47,666] [INFO] GTDB search result was written to GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/result_gtdb.tsv
[2023-06-08 08:36:47,666] [INFO] ===== GTDB Search completed =====
[2023-06-08 08:36:47,670] [INFO] DFAST_QC result json was written to GCA_902800855.1_Rumen_uncultured_genome_RUG14618_genomic.fna/dqc_result.json
[2023-06-08 08:36:47,670] [INFO] DFAST_QC completed!
[2023-06-08 08:36:47,670] [INFO] Total running time: 0h1m45s