[2023-06-08 05:20:17,844] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:20:17,846] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:20:17,847] [INFO] DQC Reference Directory: /var/lib/cwl/stgfc46d9cc-e384-4193-88f0-5378bd5a0bb7/dqc_reference
[2023-06-08 05:20:19,030] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:20:19,030] [INFO] Task started: Prodigal
[2023-06-08 05:20:19,031] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0e6b7ed-f220-49f0-b6d0-5edd4297686b/GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna.gz | prodigal -d GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/cds.fna -a GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:20:33,735] [INFO] Task succeeded: Prodigal
[2023-06-08 05:20:33,736] [INFO] Task started: HMMsearch
[2023-06-08 05:20:33,736] [INFO] Running command: hmmsearch --tblout GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgfc46d9cc-e384-4193-88f0-5378bd5a0bb7/dqc_reference/reference_markers.hmm GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:20:33,966] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:20:33,968] [INFO] Found 6/6 markers.
[2023-06-08 05:20:33,993] [INFO] Query marker FASTA was written to GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/markers.fasta
[2023-06-08 05:20:33,993] [INFO] Task started: Blastn
[2023-06-08 05:20:33,993] [INFO] Running command: blastn -query GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc46d9cc-e384-4193-88f0-5378bd5a0bb7/dqc_reference/reference_markers.fasta -out GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:20:34,636] [INFO] Task succeeded: Blastn
[2023-06-08 05:20:34,641] [INFO] Selected 27 target genomes.
[2023-06-08 05:20:34,642] [INFO] Target genome list was writen to GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/target_genomes.txt
[2023-06-08 05:20:34,643] [INFO] Task started: fastANI
[2023-06-08 05:20:34,643] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e6b7ed-f220-49f0-b6d0-5edd4297686b/GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna.gz --refList GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/target_genomes.txt --output GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:20:50,547] [INFO] Task succeeded: fastANI
[2023-06-08 05:20:50,547] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgfc46d9cc-e384-4193-88f0-5378bd5a0bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:20:50,548] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgfc46d9cc-e384-4193-88f0-5378bd5a0bb7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:20:50,556] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:20:50,557] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:20:50,557] [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
Nannocystis exedens	strain=DSM 71	GCA_002343915.1	54	54	type	True	74.9586	67	768	95	below_threshold
Nannocystis exedens	strain=ATCC 25963	GCA_900112715.1	54	54	type	True	74.9571	67	768	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:20:50,558] [INFO] DFAST Taxonomy check result was written to GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/tc_result.tsv
[2023-06-08 05:20:50,559] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:20:50,559] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:20:50,559] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgfc46d9cc-e384-4193-88f0-5378bd5a0bb7/dqc_reference/checkm_data
[2023-06-08 05:20:50,561] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:20:50,589] [INFO] Task started: CheckM
[2023-06-08 05:20:50,590] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/checkm_input GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/checkm_result
[2023-06-08 05:21:32,614] [INFO] Task succeeded: CheckM
[2023-06-08 05:21:32,616] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:21:32,644] [INFO] ===== Completeness check finished =====
[2023-06-08 05:21:32,644] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:21:32,645] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/markers.fasta)
[2023-06-08 05:21:32,645] [INFO] Task started: Blastn
[2023-06-08 05:21:32,646] [INFO] Running command: blastn -query GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/markers.fasta -db /var/lib/cwl/stgfc46d9cc-e384-4193-88f0-5378bd5a0bb7/dqc_reference/reference_markers_gtdb.fasta -out GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:21:33,622] [INFO] Task succeeded: Blastn
[2023-06-08 05:21:33,627] [INFO] Selected 13 target genomes.
[2023-06-08 05:21:33,627] [INFO] Target genome list was writen to GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:21:33,629] [INFO] Task started: fastANI
[2023-06-08 05:21:33,629] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e6b7ed-f220-49f0-b6d0-5edd4297686b/GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna.gz --refList GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/target_genomes_gtdb.txt --output GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:21:40,355] [INFO] Task succeeded: fastANI
[2023-06-08 05:21:40,376] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:21:40,376] [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_902762805.1	s__UBA1711 sp902762805	96.6386	651	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	96.86	96.86	0.85	0.85	2	conclusive
GCA_900315935.1	s__UBA1711 sp900315935	86.9428	538	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.03	97.38	0.90	0.84	6	-
GCA_902784865.1	s__UBA1711 sp902784865	84.5534	512	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.01	98.97	0.93	0.93	3	-
GCA_902782185.1	s__UBA1711 sp902782185	83.8604	462	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017940465.1	s__UBA1711 sp017940465	82.7432	465	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002394185.1	s__UBA1711 sp002394185	81.6973	304	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017501495.1	s__UBA1711 sp017501495	81.3071	317	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900314925.1	s__UBA1711 sp900314925	81.3051	392	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.65	96.66	0.91	0.86	9	-
GCA_017522105.1	s__UBA1711 sp017522105	81.102	371	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002349055.1	s__UBA1711 sp002349055	80.8861	410	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	99.90	99.90	0.97	0.97	2	-
GCA_002373995.1	s__UBA1711 sp002373995	80.6645	318	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317285.1	s__UBA1711 sp900317285	80.6442	333	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	98.22	97.84	0.89	0.83	21	-
GCA_902771735.1	s__UBA1711 sp902771735	80.5761	362	768	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__P3;g__UBA1711	95.0	97.93	97.68	0.89	0.88	5	-
--------------------------------------------------------------------------------
[2023-06-08 05:21:40,378] [INFO] GTDB search result was written to GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/result_gtdb.tsv
[2023-06-08 05:21:40,379] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:21:40,383] [INFO] DFAST_QC result json was written to GCA_902778085.1_Rumen_uncultured_genome_RUG12337_genomic.fna/dqc_result.json
[2023-06-08 05:21:40,383] [INFO] DFAST_QC completed!
[2023-06-08 05:21:40,384] [INFO] Total running time: 0h1m23s