[2023-06-08 10:14:57,645] [INFO] DFAST_QC pipeline started.
[2023-06-08 10:14:57,648] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 10:14:57,649] [INFO] DQC Reference Directory: /var/lib/cwl/stg0572a396-e987-4c50-94b6-b80a615e9861/dqc_reference
[2023-06-08 10:14:58,979] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 10:14:58,980] [INFO] Task started: Prodigal
[2023-06-08 10:14:58,981] [INFO] Running command: gunzip -c /var/lib/cwl/stgd00c984a-5153-4578-ac17-923aae41e791/GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna.gz | prodigal -d GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/cds.fna -a GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 10:15:01,946] [INFO] Task succeeded: Prodigal
[2023-06-08 10:15:01,946] [INFO] Task started: HMMsearch
[2023-06-08 10:15:01,946] [INFO] Running command: hmmsearch --tblout GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0572a396-e987-4c50-94b6-b80a615e9861/dqc_reference/reference_markers.hmm GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/protein.faa > /dev/null
[2023-06-08 10:15:02,103] [INFO] Task succeeded: HMMsearch
[2023-06-08 10:15:02,104] [INFO] Found 6/6 markers.
[2023-06-08 10:15:02,121] [INFO] Query marker FASTA was written to GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/markers.fasta
[2023-06-08 10:15:02,122] [INFO] Task started: Blastn
[2023-06-08 10:15:02,122] [INFO] Running command: blastn -query GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/markers.fasta -db /var/lib/cwl/stg0572a396-e987-4c50-94b6-b80a615e9861/dqc_reference/reference_markers.fasta -out GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:15:02,692] [INFO] Task succeeded: Blastn
[2023-06-08 10:15:02,696] [INFO] Selected 16 target genomes.
[2023-06-08 10:15:02,697] [INFO] Target genome list was writen to GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/target_genomes.txt
[2023-06-08 10:15:02,698] [INFO] Task started: fastANI
[2023-06-08 10:15:02,699] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00c984a-5153-4578-ac17-923aae41e791/GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna.gz --refList GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/target_genomes.txt --output GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 10:15:08,918] [INFO] Task succeeded: fastANI
[2023-06-08 10:15:08,919] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0572a396-e987-4c50-94b6-b80a615e9861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 10:15:08,919] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0572a396-e987-4c50-94b6-b80a615e9861/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 10:15:08,921] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 10:15:08,921] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 10:15:08,921] [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 10:15:08,922] [INFO] DFAST Taxonomy check result was written to GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/tc_result.tsv
[2023-06-08 10:15:08,923] [INFO] ===== Taxonomy check completed =====
[2023-06-08 10:15:08,923] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 10:15:08,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0572a396-e987-4c50-94b6-b80a615e9861/dqc_reference/checkm_data
[2023-06-08 10:15:08,926] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 10:15:08,945] [INFO] Task started: CheckM
[2023-06-08 10:15:08,946] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/checkm_input GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/checkm_result
[2023-06-08 10:15:24,923] [INFO] Task succeeded: CheckM
[2023-06-08 10:15:24,924] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.30%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 10:15:24,937] [INFO] ===== Completeness check finished =====
[2023-06-08 10:15:24,937] [INFO] ===== Start GTDB Search =====
[2023-06-08 10:15:24,937] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/markers.fasta)
[2023-06-08 10:15:24,937] [INFO] Task started: Blastn
[2023-06-08 10:15:24,937] [INFO] Running command: blastn -query GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/markers.fasta -db /var/lib/cwl/stg0572a396-e987-4c50-94b6-b80a615e9861/dqc_reference/reference_markers_gtdb.fasta -out GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 10:15:25,739] [INFO] Task succeeded: Blastn
[2023-06-08 10:15:25,743] [INFO] Selected 12 target genomes.
[2023-06-08 10:15:25,743] [INFO] Target genome list was writen to GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 10:15:25,747] [INFO] Task started: fastANI
[2023-06-08 10:15:25,747] [INFO] Running command: fastANI --query /var/lib/cwl/stgd00c984a-5153-4578-ac17-923aae41e791/GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna.gz --refList GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/target_genomes_gtdb.txt --output GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 10:15:30,205] [INFO] Task succeeded: fastANI
[2023-06-08 10:15:30,221] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 10:15:30,222] [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_902766975.1	s__UBA2813 sp902766975	100.0	485	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	98.60	98.29	0.95	0.95	3	conclusive
GCA_902802825.1	s__UBA2813 sp902802825	81.3578	317	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765655.1	s__UBA2813 sp902765655	80.8964	265	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902774905.1	s__UBA2813 sp902774905	80.4543	338	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	97.89	97.89	0.91	0.91	2	-
GCA_017470815.1	s__UBA2813 sp017470815	80.307	327	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902792085.1	s__UBA2813 sp902792085	80.2005	332	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902777855.1	s__UBA2813 sp902777855	79.7184	312	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902794035.1	s__UBA2813 sp902794035	79.6069	286	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902788345.1	s__UBA2813 sp902788345	77.9162	212	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017477685.1	s__UBA2813 sp017477685	77.7873	90	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900319365.1	s__UBA2813 sp900319365	77.4902	162	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	99.78	99.51	0.97	0.93	7	-
GCA_017941035.1	s__UBA2813 sp017941035	77.3904	159	493	d__Bacteria;p__Cyanobacteria;c__Vampirovibrionia;o__Gastranaerophilales;f__Gastranaerophilaceae;g__UBA2813	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 10:15:30,223] [INFO] GTDB search result was written to GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/result_gtdb.tsv
[2023-06-08 10:15:30,224] [INFO] ===== GTDB Search completed =====
[2023-06-08 10:15:30,227] [INFO] DFAST_QC result json was written to GCA_902766975.1_Rumen_uncultured_genome_RUG11206_genomic.fna/dqc_result.json
[2023-06-08 10:15:30,227] [INFO] DFAST_QC completed!
[2023-06-08 10:15:30,227] [INFO] Total running time: 0h0m33s