[2023-06-07 22:55:30,277] [INFO] DFAST_QC pipeline started.
[2023-06-07 22:55:30,283] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 22:55:30,283] [INFO] DQC Reference Directory: /var/lib/cwl/stgd444e9a2-efe7-454e-9580-d5790534f116/dqc_reference
[2023-06-07 22:55:32,284] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 22:55:32,285] [INFO] Task started: Prodigal
[2023-06-07 22:55:32,285] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ccdaddd-a3ad-47cd-adf5-63784ed06c32/GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna.gz | prodigal -d GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/cds.fna -a GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 22:55:54,464] [INFO] Task succeeded: Prodigal
[2023-06-07 22:55:54,465] [INFO] Task started: HMMsearch
[2023-06-07 22:55:54,465] [INFO] Running command: hmmsearch --tblout GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd444e9a2-efe7-454e-9580-d5790534f116/dqc_reference/reference_markers.hmm GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/protein.faa > /dev/null
[2023-06-07 22:55:54,722] [INFO] Task succeeded: HMMsearch
[2023-06-07 22:55:54,723] [INFO] Found 6/6 markers.
[2023-06-07 22:55:54,754] [INFO] Query marker FASTA was written to GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/markers.fasta
[2023-06-07 22:55:54,754] [INFO] Task started: Blastn
[2023-06-07 22:55:54,754] [INFO] Running command: blastn -query GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/markers.fasta -db /var/lib/cwl/stgd444e9a2-efe7-454e-9580-d5790534f116/dqc_reference/reference_markers.fasta -out GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:55:55,345] [INFO] Task succeeded: Blastn
[2023-06-07 22:55:55,352] [INFO] Selected 24 target genomes.
[2023-06-07 22:55:55,352] [INFO] Target genome list was writen to GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/target_genomes.txt
[2023-06-07 22:55:55,356] [INFO] Task started: fastANI
[2023-06-07 22:55:55,356] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ccdaddd-a3ad-47cd-adf5-63784ed06c32/GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna.gz --refList GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/target_genomes.txt --output GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 22:56:09,884] [INFO] Task succeeded: fastANI
[2023-06-07 22:56:09,885] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd444e9a2-efe7-454e-9580-d5790534f116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 22:56:09,885] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd444e9a2-efe7-454e-9580-d5790534f116/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 22:56:09,890] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 22:56:09,890] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 22:56:09,890] [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_009676955.1	2606626	2606626	type	True	77.7222	184	1058	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009696565.1	2606626	2606626	type	True	77.7074	178	1058	95	below_threshold
Barnesiella viscericola	strain=C46, DSM 18177	GCA_000512915.1	397865	397865	type	True	75.799	55	1058	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 22:56:09,892] [INFO] DFAST Taxonomy check result was written to GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/tc_result.tsv
[2023-06-07 22:56:09,893] [INFO] ===== Taxonomy check completed =====
[2023-06-07 22:56:09,893] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 22:56:09,893] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd444e9a2-efe7-454e-9580-d5790534f116/dqc_reference/checkm_data
[2023-06-07 22:56:09,894] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 22:56:09,934] [INFO] Task started: CheckM
[2023-06-07 22:56:09,934] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/checkm_input GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/checkm_result
[2023-06-07 22:57:13,728] [INFO] Task succeeded: CheckM
[2023-06-07 22:57:13,730] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-07 22:57:13,758] [INFO] ===== Completeness check finished =====
[2023-06-07 22:57:13,758] [INFO] ===== Start GTDB Search =====
[2023-06-07 22:57:13,759] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/markers.fasta)
[2023-06-07 22:57:13,759] [INFO] Task started: Blastn
[2023-06-07 22:57:13,760] [INFO] Running command: blastn -query GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/markers.fasta -db /var/lib/cwl/stgd444e9a2-efe7-454e-9580-d5790534f116/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 22:57:14,617] [INFO] Task succeeded: Blastn
[2023-06-07 22:57:14,622] [INFO] Selected 9 target genomes.
[2023-06-07 22:57:14,622] [INFO] Target genome list was writen to GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 22:57:14,628] [INFO] Task started: fastANI
[2023-06-07 22:57:14,628] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ccdaddd-a3ad-47cd-adf5-63784ed06c32/GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna.gz --refList GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/target_genomes_gtdb.txt --output GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 22:57:20,467] [INFO] Task succeeded: fastANI
[2023-06-07 22:57:20,481] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 22:57:20,481] [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_002396085.1	s__Sodaliphilus sp002396085	97.7676	788	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.76	97.72	0.87	0.86	3	conclusive
GCA_902781045.1	s__Sodaliphilus sp902781045	84.7632	715	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.92	97.92	0.86	0.86	2	-
GCA_002353885.1	s__Sodaliphilus sp002353885	84.0281	626	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.50	97.13	0.86	0.82	5	-
GCA_017477555.1	s__Sodaliphilus sp017477555	83.7388	604	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.74	97.72	0.83	0.78	3	-
GCA_016290765.1	s__Sodaliphilus sp016290765	80.578	462	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017557285.1	s__Sodaliphilus sp017557285	80.4783	322	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016281825.1	s__Sodaliphilus sp016281825	79.9121	426	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017545095.1	s__Sodaliphilus sp017545095	77.8141	280	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018065815.1	s__Sodaliphilus sp018065815	77.4548	165	1058	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-07 22:57:20,483] [INFO] GTDB search result was written to GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/result_gtdb.tsv
[2023-06-07 22:57:20,484] [INFO] ===== GTDB Search completed =====
[2023-06-07 22:57:20,487] [INFO] DFAST_QC result json was written to GCA_902763945.1_Rumen_uncultured_genome_RUG10912_genomic.fna/dqc_result.json
[2023-06-07 22:57:20,487] [INFO] DFAST_QC completed!
[2023-06-07 22:57:20,487] [INFO] Total running time: 0h1m50s