[2023-06-08 18:25:02,139] [INFO] DFAST_QC pipeline started.
[2023-06-08 18:25:02,143] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 18:25:02,143] [INFO] DQC Reference Directory: /var/lib/cwl/stg8e85a276-4c6e-45fa-b4a9-e57ee65023a2/dqc_reference
[2023-06-08 18:25:03,461] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 18:25:03,462] [INFO] Task started: Prodigal
[2023-06-08 18:25:03,463] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a8c4cd0-b083-4302-98fb-224c55f811db/GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna.gz | prodigal -d GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/cds.fna -a GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 18:25:10,673] [INFO] Task succeeded: Prodigal
[2023-06-08 18:25:10,673] [INFO] Task started: HMMsearch
[2023-06-08 18:25:10,673] [INFO] Running command: hmmsearch --tblout GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8e85a276-4c6e-45fa-b4a9-e57ee65023a2/dqc_reference/reference_markers.hmm GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/protein.faa > /dev/null
[2023-06-08 18:25:10,929] [INFO] Task succeeded: HMMsearch
[2023-06-08 18:25:10,930] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg4a8c4cd0-b083-4302-98fb-224c55f811db/GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna.gz]
[2023-06-08 18:25:10,957] [INFO] Query marker FASTA was written to GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/markers.fasta
[2023-06-08 18:25:10,958] [INFO] Task started: Blastn
[2023-06-08 18:25:10,958] [INFO] Running command: blastn -query GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e85a276-4c6e-45fa-b4a9-e57ee65023a2/dqc_reference/reference_markers.fasta -out GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:25:11,542] [INFO] Task succeeded: Blastn
[2023-06-08 18:25:11,546] [INFO] Selected 17 target genomes.
[2023-06-08 18:25:11,547] [INFO] Target genome list was writen to GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/target_genomes.txt
[2023-06-08 18:25:11,549] [INFO] Task started: fastANI
[2023-06-08 18:25:11,549] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a8c4cd0-b083-4302-98fb-224c55f811db/GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna.gz --refList GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/target_genomes.txt --output GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 18:25:22,085] [INFO] Task succeeded: fastANI
[2023-06-08 18:25:22,086] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8e85a276-4c6e-45fa-b4a9-e57ee65023a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 18:25:22,087] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8e85a276-4c6e-45fa-b4a9-e57ee65023a2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 18:25:22,089] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 18:25:22,089] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 18:25:22,089] [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 18:25:22,091] [INFO] DFAST Taxonomy check result was written to GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/tc_result.tsv
[2023-06-08 18:25:22,091] [INFO] ===== Taxonomy check completed =====
[2023-06-08 18:25:22,092] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 18:25:22,092] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8e85a276-4c6e-45fa-b4a9-e57ee65023a2/dqc_reference/checkm_data
[2023-06-08 18:25:22,095] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 18:25:22,126] [INFO] Task started: CheckM
[2023-06-08 18:25:22,126] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/checkm_input GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/checkm_result
[2023-06-08 18:25:49,582] [INFO] Task succeeded: CheckM
[2023-06-08 18:25:49,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 72.92%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 18:25:49,607] [INFO] ===== Completeness check finished =====
[2023-06-08 18:25:49,607] [INFO] ===== Start GTDB Search =====
[2023-06-08 18:25:49,608] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/markers.fasta)
[2023-06-08 18:25:49,608] [INFO] Task started: Blastn
[2023-06-08 18:25:49,608] [INFO] Running command: blastn -query GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/markers.fasta -db /var/lib/cwl/stg8e85a276-4c6e-45fa-b4a9-e57ee65023a2/dqc_reference/reference_markers_gtdb.fasta -out GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 18:25:50,363] [INFO] Task succeeded: Blastn
[2023-06-08 18:25:50,368] [INFO] Selected 14 target genomes.
[2023-06-08 18:25:50,369] [INFO] Target genome list was writen to GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 18:25:50,374] [INFO] Task started: fastANI
[2023-06-08 18:25:50,374] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a8c4cd0-b083-4302-98fb-224c55f811db/GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna.gz --refList GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/target_genomes_gtdb.txt --output GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 18:25:57,874] [INFO] Task succeeded: fastANI
[2023-06-08 18:25:57,891] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 18:25:57,891] [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_900319245.1	s__CAG-791 sp900319245	98.2501	699	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.27	97.33	0.84	0.77	7	conclusive
GCA_902801415.1	s__CAG-791 sp902801415	86.3884	524	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.60	97.44	0.77	0.76	3	-
GCA_902794825.1	s__CAG-791 sp902794825	81.7574	365	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.56	96.51	0.79	0.74	7	-
GCA_002448395.1	s__CAG-791 sp002448395	81.3574	298	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785055.1	s__CAG-791 sp902785055	81.336	348	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.92	97.83	0.74	0.74	3	-
GCA_902781325.1	s__CAG-791 sp902781325	81.0804	360	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	97.79	97.38	0.80	0.79	3	-
GCA_002395235.1	s__CAG-791 sp002395235	80.9971	395	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017469935.1	s__CAG-791 sp017469935	80.5304	443	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003447895.1	s__CAG-791 sp003447895	79.9119	277	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902801585.1	s__CAG-791 sp902801585	79.6344	353	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767235.1	s__CAG-791 sp902767235	79.5402	243	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902768735.1	s__CAG-791 sp900320335	79.3878	307	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	99.71	99.71	0.85	0.85	2	-
GCA_900321785.1	s__CAG-791 sp900321785	78.4965	100	838	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Lachnospirales;f__Lachnospiraceae;g__CAG-791	95.0	98.92	97.67	0.83	0.75	9	-
--------------------------------------------------------------------------------
[2023-06-08 18:25:57,893] [INFO] GTDB search result was written to GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/result_gtdb.tsv
[2023-06-08 18:25:57,894] [INFO] ===== GTDB Search completed =====
[2023-06-08 18:25:57,897] [INFO] DFAST_QC result json was written to GCA_902763385.1_Rumen_uncultured_genome_RUG10847_genomic.fna/dqc_result.json
[2023-06-08 18:25:57,898] [INFO] DFAST_QC completed!
[2023-06-08 18:25:57,898] [INFO] Total running time: 0h0m56s