[2023-06-08 19:34:10,961] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:34:10,963] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:34:10,963] [INFO] DQC Reference Directory: /var/lib/cwl/stge31a43e2-d8dd-43f9-92e0-1b3955f152be/dqc_reference
[2023-06-08 19:34:13,690] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:34:13,691] [INFO] Task started: Prodigal
[2023-06-08 19:34:13,691] [INFO] Running command: gunzip -c /var/lib/cwl/stgab757537-1778-4dd1-ba93-39ad4f5f8e55/GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna.gz | prodigal -d GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/cds.fna -a GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:34:36,434] [INFO] Task succeeded: Prodigal
[2023-06-08 19:34:36,434] [INFO] Task started: HMMsearch
[2023-06-08 19:34:36,434] [INFO] Running command: hmmsearch --tblout GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge31a43e2-d8dd-43f9-92e0-1b3955f152be/dqc_reference/reference_markers.hmm GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:34:36,676] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:34:36,677] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgab757537-1778-4dd1-ba93-39ad4f5f8e55/GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna.gz]
[2023-06-08 19:34:36,707] [INFO] Query marker FASTA was written to GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/markers.fasta
[2023-06-08 19:34:36,707] [INFO] Task started: Blastn
[2023-06-08 19:34:36,707] [INFO] Running command: blastn -query GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/markers.fasta -db /var/lib/cwl/stge31a43e2-d8dd-43f9-92e0-1b3955f152be/dqc_reference/reference_markers.fasta -out GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:34:37,369] [INFO] Task succeeded: Blastn
[2023-06-08 19:34:37,374] [INFO] Selected 23 target genomes.
[2023-06-08 19:34:37,375] [INFO] Target genome list was writen to GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/target_genomes.txt
[2023-06-08 19:34:37,377] [INFO] Task started: fastANI
[2023-06-08 19:34:37,378] [INFO] Running command: fastANI --query /var/lib/cwl/stgab757537-1778-4dd1-ba93-39ad4f5f8e55/GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna.gz --refList GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/target_genomes.txt --output GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:34:51,593] [INFO] Task succeeded: fastANI
[2023-06-08 19:34:51,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge31a43e2-d8dd-43f9-92e0-1b3955f152be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:34:51,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge31a43e2-d8dd-43f9-92e0-1b3955f152be/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:34:51,598] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:34:51,598] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 19:34:51,598] [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	78.0486	196	1080	95	below_threshold
Sodaliphilus pleomorphus	strain=Oil-RF-744-WCA-WT-10	GCA_009676955.1	2606626	2606626	type	True	77.9921	201	1080	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 19:34:51,600] [INFO] DFAST Taxonomy check result was written to GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/tc_result.tsv
[2023-06-08 19:34:51,600] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:34:51,601] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:34:51,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge31a43e2-d8dd-43f9-92e0-1b3955f152be/dqc_reference/checkm_data
[2023-06-08 19:34:51,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:34:51,643] [INFO] Task started: CheckM
[2023-06-08 19:34:51,643] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/checkm_input GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/checkm_result
[2023-06-08 19:35:55,993] [INFO] Task succeeded: CheckM
[2023-06-08 19:35:55,995] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:35:56,016] [INFO] ===== Completeness check finished =====
[2023-06-08 19:35:56,016] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:35:56,017] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/markers.fasta)
[2023-06-08 19:35:56,017] [INFO] Task started: Blastn
[2023-06-08 19:35:56,017] [INFO] Running command: blastn -query GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/markers.fasta -db /var/lib/cwl/stge31a43e2-d8dd-43f9-92e0-1b3955f152be/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:35:57,111] [INFO] Task succeeded: Blastn
[2023-06-08 19:35:57,115] [INFO] Selected 11 target genomes.
[2023-06-08 19:35:57,116] [INFO] Target genome list was writen to GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:35:57,118] [INFO] Task started: fastANI
[2023-06-08 19:35:57,118] [INFO] Running command: fastANI --query /var/lib/cwl/stgab757537-1778-4dd1-ba93-39ad4f5f8e55/GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna.gz --refList GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/target_genomes_gtdb.txt --output GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:36:05,823] [INFO] Task succeeded: fastANI
[2023-06-08 19:36:05,837] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:36:05,837] [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_002353885.1	s__Sodaliphilus sp002353885	97.5936	823	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.50	97.13	0.86	0.82	5	conclusive
GCA_902781045.1	s__Sodaliphilus sp902781045	85.8252	767	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.92	97.92	0.86	0.86	2	-
GCA_002396085.1	s__Sodaliphilus sp002396085	84.3654	623	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.76	97.72	0.87	0.86	3	-
GCA_017477555.1	s__Sodaliphilus sp017477555	84.0617	632	1080	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	80.2844	467	1080	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	80.1517	333	1080	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	79.9182	410	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902776835.1	s__Sodaliphilus sp902776835	78.6559	324	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	97.85	97.41	0.91	0.88	8	-
GCA_900318865.1	s__Sodaliphilus sp900318865	78.1166	263	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.72	97.82	0.92	0.87	5	-
GCA_902782465.1	s__Sodaliphilus sp902782465	77.9741	266	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	98.05	98.05	0.87	0.87	2	-
GCA_902784675.1	s__Sodaliphilus sp902784675	77.6597	230	1080	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Muribaculaceae;g__Sodaliphilus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:36:05,840] [INFO] GTDB search result was written to GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/result_gtdb.tsv
[2023-06-08 19:36:05,840] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:36:05,844] [INFO] DFAST_QC result json was written to GCA_902778475.1_Rumen_uncultured_genome_RUG12371_genomic.fna/dqc_result.json
[2023-06-08 19:36:05,844] [INFO] DFAST_QC completed!
[2023-06-08 19:36:05,844] [INFO] Total running time: 0h1m55s