[2023-06-05 13:00:21,311] [INFO] DFAST_QC pipeline started.
[2023-06-05 13:00:21,315] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 13:00:21,315] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ac46a06-91f6-4fc6-9361-7160ad159242/dqc_reference
[2023-06-05 13:00:22,714] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 13:00:22,715] [INFO] Task started: Prodigal
[2023-06-05 13:00:22,715] [INFO] Running command: gunzip -c /var/lib/cwl/stg12a10c2e-1d24-4ff0-9a61-c61d02700bdd/GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna.gz | prodigal -d GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/cds.fna -a GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 13:00:42,050] [INFO] Task succeeded: Prodigal
[2023-06-05 13:00:42,050] [INFO] Task started: HMMsearch
[2023-06-05 13:00:42,050] [INFO] Running command: hmmsearch --tblout GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ac46a06-91f6-4fc6-9361-7160ad159242/dqc_reference/reference_markers.hmm GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/protein.faa > /dev/null
[2023-06-05 13:00:42,296] [INFO] Task succeeded: HMMsearch
[2023-06-05 13:00:42,297] [INFO] Found 6/6 markers.
[2023-06-05 13:00:42,325] [INFO] Query marker FASTA was written to GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/markers.fasta
[2023-06-05 13:00:42,326] [INFO] Task started: Blastn
[2023-06-05 13:00:42,326] [INFO] Running command: blastn -query GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ac46a06-91f6-4fc6-9361-7160ad159242/dqc_reference/reference_markers.fasta -out GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:00:42,927] [INFO] Task succeeded: Blastn
[2023-06-05 13:00:42,934] [INFO] Selected 29 target genomes.
[2023-06-05 13:00:42,935] [INFO] Target genome list was writen to GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/target_genomes.txt
[2023-06-05 13:00:42,938] [INFO] Task started: fastANI
[2023-06-05 13:00:42,938] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a10c2e-1d24-4ff0-9a61-c61d02700bdd/GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna.gz --refList GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/target_genomes.txt --output GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 13:01:01,323] [INFO] Task succeeded: fastANI
[2023-06-05 13:01:01,323] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ac46a06-91f6-4fc6-9361-7160ad159242/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 13:01:01,324] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ac46a06-91f6-4fc6-9361-7160ad159242/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 13:01:01,326] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 13:01:01,326] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 13:01:01,326] [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
--------------------------------------------------------------------------------
[2023-06-05 13:01:01,328] [INFO] DFAST Taxonomy check result was written to GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/tc_result.tsv
[2023-06-05 13:01:01,328] [INFO] ===== Taxonomy check completed =====
[2023-06-05 13:01:01,328] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 13:01:01,329] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ac46a06-91f6-4fc6-9361-7160ad159242/dqc_reference/checkm_data
[2023-06-05 13:01:01,331] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 13:01:01,361] [INFO] Task started: CheckM
[2023-06-05 13:01:01,361] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/checkm_input GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/checkm_result
[2023-06-05 13:01:54,595] [INFO] Task succeeded: CheckM
[2023-06-05 13:01:54,596] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 13:01:54,615] [INFO] ===== Completeness check finished =====
[2023-06-05 13:01:54,616] [INFO] ===== Start GTDB Search =====
[2023-06-05 13:01:54,616] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/markers.fasta)
[2023-06-05 13:01:54,616] [INFO] Task started: Blastn
[2023-06-05 13:01:54,616] [INFO] Running command: blastn -query GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ac46a06-91f6-4fc6-9361-7160ad159242/dqc_reference/reference_markers_gtdb.fasta -out GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 13:01:55,436] [INFO] Task succeeded: Blastn
[2023-06-05 13:01:55,440] [INFO] Selected 13 target genomes.
[2023-06-05 13:01:55,440] [INFO] Target genome list was writen to GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 13:01:55,445] [INFO] Task started: fastANI
[2023-06-05 13:01:55,445] [INFO] Running command: fastANI --query /var/lib/cwl/stg12a10c2e-1d24-4ff0-9a61-c61d02700bdd/GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna.gz --refList GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/target_genomes_gtdb.txt --output GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 13:02:04,262] [INFO] Task succeeded: fastANI
[2023-06-05 13:02:04,273] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 13:02:04,273] [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_902791165.1	s__Limimorpha sp902791165	96.4926	689	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	96.39	95.84	0.84	0.78	7	conclusive
GCA_900321315.1	s__Limimorpha sp900321315	86.207	492	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	100.00	100.00	0.98	0.98	2	-
GCA_902785755.1	s__Limimorpha sp902785755	84.7013	579	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.44	95.41	0.82	0.81	3	-
GCA_902770835.1	s__Limimorpha sp902770835	84.4186	541	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	95.42	95.03	0.80	0.78	4	-
GCA_902769815.1	s__Limimorpha sp902769815	83.9832	463	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902769875.1	s__Limimorpha sp902769875	83.7094	521	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_905233685.1	s__Limimorpha sp905233685	83.558	532	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318465.1	s__Limimorpha sp900318465	83.3808	502	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.54	95.09	0.89	0.78	3	-
GCA_017439405.1	s__Limimorpha sp017439405	82.7129	497	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017477425.1	s__Limimorpha sp017477425	81.9031	493	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002396205.1	s__Limimorpha sp002396205	81.6651	487	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017460915.1	s__Limimorpha sp017460915	81.3929	426	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900318085.1	s__Limimorpha sp900318085	81.2808	471	905	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__F082;g__Limimorpha	95.0	97.28	96.84	0.87	0.80	12	-
--------------------------------------------------------------------------------
[2023-06-05 13:02:04,275] [INFO] GTDB search result was written to GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/result_gtdb.tsv
[2023-06-05 13:02:04,275] [INFO] ===== GTDB Search completed =====
[2023-06-05 13:02:04,278] [INFO] DFAST_QC result json was written to GCA_902791365.1_Rumen_uncultured_genome_RUG13663_genomic.fna/dqc_result.json
[2023-06-05 13:02:04,278] [INFO] DFAST_QC completed!
[2023-06-05 13:02:04,279] [INFO] Total running time: 0h1m43s