[2023-06-08 13:48:31,012] [INFO] DFAST_QC pipeline started.
[2023-06-08 13:48:31,014] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 13:48:31,014] [INFO] DQC Reference Directory: /var/lib/cwl/stgf5bd65fb-3a20-4f75-a29f-3668e6758d30/dqc_reference
[2023-06-08 13:48:32,297] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 13:48:32,298] [INFO] Task started: Prodigal
[2023-06-08 13:48:32,298] [INFO] Running command: gunzip -c /var/lib/cwl/stgf0e267b1-18f8-49c1-8197-039913b29b05/GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna.gz | prodigal -d GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/cds.fna -a GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 13:48:43,943] [INFO] Task succeeded: Prodigal
[2023-06-08 13:48:43,944] [INFO] Task started: HMMsearch
[2023-06-08 13:48:43,944] [INFO] Running command: hmmsearch --tblout GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf5bd65fb-3a20-4f75-a29f-3668e6758d30/dqc_reference/reference_markers.hmm GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/protein.faa > /dev/null
[2023-06-08 13:48:44,194] [INFO] Task succeeded: HMMsearch
[2023-06-08 13:48:44,195] [INFO] Found 6/6 markers.
[2023-06-08 13:48:44,223] [INFO] Query marker FASTA was written to GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/markers.fasta
[2023-06-08 13:48:44,223] [INFO] Task started: Blastn
[2023-06-08 13:48:44,223] [INFO] Running command: blastn -query GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5bd65fb-3a20-4f75-a29f-3668e6758d30/dqc_reference/reference_markers.fasta -out GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:48:44,802] [INFO] Task succeeded: Blastn
[2023-06-08 13:48:44,807] [INFO] Selected 26 target genomes.
[2023-06-08 13:48:44,808] [INFO] Target genome list was writen to GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/target_genomes.txt
[2023-06-08 13:48:44,810] [INFO] Task started: fastANI
[2023-06-08 13:48:44,810] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e267b1-18f8-49c1-8197-039913b29b05/GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna.gz --refList GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/target_genomes.txt --output GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 13:49:05,409] [INFO] Task succeeded: fastANI
[2023-06-08 13:49:05,410] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf5bd65fb-3a20-4f75-a29f-3668e6758d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 13:49:05,410] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf5bd65fb-3a20-4f75-a29f-3668e6758d30/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 13:49:05,412] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 13:49:05,412] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 13:49:05,413] [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
--------------------------------------------------------------------------------
[2023-06-08 13:49:05,415] [INFO] DFAST Taxonomy check result was written to GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/tc_result.tsv
[2023-06-08 13:49:05,416] [INFO] ===== Taxonomy check completed =====
[2023-06-08 13:49:05,416] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 13:49:05,416] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf5bd65fb-3a20-4f75-a29f-3668e6758d30/dqc_reference/checkm_data
[2023-06-08 13:49:05,421] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 13:49:05,447] [INFO] Task started: CheckM
[2023-06-08 13:49:05,447] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/checkm_input GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/checkm_result
[2023-06-08 13:49:42,158] [INFO] Task succeeded: CheckM
[2023-06-08 13:49:42,159] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.88%
Contamintation: 11.11%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 13:49:42,181] [INFO] ===== Completeness check finished =====
[2023-06-08 13:49:42,181] [INFO] ===== Start GTDB Search =====
[2023-06-08 13:49:42,182] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/markers.fasta)
[2023-06-08 13:49:42,182] [INFO] Task started: Blastn
[2023-06-08 13:49:42,182] [INFO] Running command: blastn -query GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/markers.fasta -db /var/lib/cwl/stgf5bd65fb-3a20-4f75-a29f-3668e6758d30/dqc_reference/reference_markers_gtdb.fasta -out GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 13:49:43,035] [INFO] Task succeeded: Blastn
[2023-06-08 13:49:43,040] [INFO] Selected 17 target genomes.
[2023-06-08 13:49:43,040] [INFO] Target genome list was writen to GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 13:49:43,045] [INFO] Task started: fastANI
[2023-06-08 13:49:43,045] [INFO] Running command: fastANI --query /var/lib/cwl/stgf0e267b1-18f8-49c1-8197-039913b29b05/GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna.gz --refList GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/target_genomes_gtdb.txt --output GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 13:49:51,550] [INFO] Task succeeded: fastANI
[2023-06-08 13:49:51,568] [INFO] Found 17 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 13:49:51,568] [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_902774995.1	s__RF16 sp902774995	100.0	664	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	95.68	95.65	0.72	0.66	3	conclusive
GCA_902799185.1	s__RF16 sp902799185	92.6625	530	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002369075.1	s__RF16 sp002369075	81.9117	271	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233255.1	s__RF16 sp905233255	81.3331	315	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002373505.1	s__RF16 sp002373505	80.9312	322	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.32	96.25	0.84	0.83	3	-
GCA_002394395.1	s__RF16 sp002394395	80.6101	239	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316845.1	s__RF16 sp900316845	80.4869	283	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.47	95.23	0.82	0.74	5	-
GCA_900321605.1	s__RF16 sp900321605	80.3321	285	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.88	95.40	0.80	0.70	4	-
GCA_017471285.1	s__RF16 sp017471285	80.2084	180	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.11	96.11	0.57	0.57	2	-
GCA_002354055.1	s__RF16 sp002354055	80.1707	301	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	95.95	95.67	0.83	0.82	3	-
GCA_902792535.1	s__RF16 sp902792535	80.1631	297	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478725.1	s__RF16 sp017478725	80.0334	252	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017542915.1	s__RF16 sp017542915	79.7614	236	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017478035.1	s__RF16 sp017478035	79.6914	205	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319035.1	s__RF16 sp900319035	79.611	275	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.02	95.23	0.81	0.72	10	-
GCA_902799555.1	s__RF16 sp902799555	79.1418	223	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	96.18	96.01	0.81	0.78	3	-
GCA_017541805.1	s__RF16 sp017541805	78.1905	174	668	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Paludibacteraceae;g__RF16	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 13:49:51,570] [INFO] GTDB search result was written to GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/result_gtdb.tsv
[2023-06-08 13:49:51,571] [INFO] ===== GTDB Search completed =====
[2023-06-08 13:49:51,574] [INFO] DFAST_QC result json was written to GCA_902774995.1_Rumen_uncultured_genome_RUG12032_genomic.fna/dqc_result.json
[2023-06-08 13:49:51,574] [INFO] DFAST_QC completed!
[2023-06-08 13:49:51,574] [INFO] Total running time: 0h1m21s