[2023-06-08 05:33:17,799] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:33:17,802] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:33:17,802] [INFO] DQC Reference Directory: /var/lib/cwl/stg3e247521-8ebb-420a-a4aa-716b3c879333/dqc_reference
[2023-06-08 05:33:20,249] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:33:20,249] [INFO] Task started: Prodigal
[2023-06-08 05:33:20,250] [INFO] Running command: gunzip -c /var/lib/cwl/stg02165470-94ed-4cfb-bbec-26a0837615a0/GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna.gz | prodigal -d GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/cds.fna -a GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:33:22,325] [INFO] Task succeeded: Prodigal
[2023-06-08 05:33:22,325] [INFO] Task started: HMMsearch
[2023-06-08 05:33:22,325] [INFO] Running command: hmmsearch --tblout GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3e247521-8ebb-420a-a4aa-716b3c879333/dqc_reference/reference_markers.hmm GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:33:22,547] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:33:22,549] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg02165470-94ed-4cfb-bbec-26a0837615a0/GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna.gz]
[2023-06-08 05:33:22,568] [INFO] Query marker FASTA was written to GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/markers.fasta
[2023-06-08 05:33:22,569] [INFO] Task started: Blastn
[2023-06-08 05:33:22,569] [INFO] Running command: blastn -query GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e247521-8ebb-420a-a4aa-716b3c879333/dqc_reference/reference_markers.fasta -out GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:33:23,800] [INFO] Task succeeded: Blastn
[2023-06-08 05:33:23,808] [INFO] Selected 26 target genomes.
[2023-06-08 05:33:23,809] [INFO] Target genome list was writen to GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/target_genomes.txt
[2023-06-08 05:33:23,813] [INFO] Task started: fastANI
[2023-06-08 05:33:23,813] [INFO] Running command: fastANI --query /var/lib/cwl/stg02165470-94ed-4cfb-bbec-26a0837615a0/GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna.gz --refList GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/target_genomes.txt --output GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:33:33,093] [INFO] Task succeeded: fastANI
[2023-06-08 05:33:33,093] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3e247521-8ebb-420a-a4aa-716b3c879333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:33:33,094] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3e247521-8ebb-420a-a4aa-716b3c879333/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:33:33,096] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:33:33,096] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 05:33:33,096] [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 05:33:33,099] [INFO] DFAST Taxonomy check result was written to GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/tc_result.tsv
[2023-06-08 05:33:33,099] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:33:33,099] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:33:33,100] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3e247521-8ebb-420a-a4aa-716b3c879333/dqc_reference/checkm_data
[2023-06-08 05:33:33,103] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:33:33,124] [INFO] Task started: CheckM
[2023-06-08 05:33:33,125] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/checkm_input GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/checkm_result
[2023-06-08 05:33:47,651] [INFO] Task succeeded: CheckM
[2023-06-08 05:33:47,652] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:33:47,672] [INFO] ===== Completeness check finished =====
[2023-06-08 05:33:47,672] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:33:47,673] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/markers.fasta)
[2023-06-08 05:33:47,673] [INFO] Task started: Blastn
[2023-06-08 05:33:47,673] [INFO] Running command: blastn -query GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/markers.fasta -db /var/lib/cwl/stg3e247521-8ebb-420a-a4aa-716b3c879333/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:33:48,400] [INFO] Task succeeded: Blastn
[2023-06-08 05:33:48,405] [INFO] Selected 24 target genomes.
[2023-06-08 05:33:48,405] [INFO] Target genome list was writen to GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:33:48,413] [INFO] Task started: fastANI
[2023-06-08 05:33:48,413] [INFO] Running command: fastANI --query /var/lib/cwl/stg02165470-94ed-4cfb-bbec-26a0837615a0/GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna.gz --refList GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/target_genomes_gtdb.txt --output GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:33:54,255] [INFO] Task succeeded: fastANI
[2023-06-08 05:33:54,261] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:33:54,261] [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_902787955.1	s__UBA3207 sp902787955	95.9773	355	391	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	95.98	95.98	0.91	0.91	2	conclusive
GCA_902797855.1	s__UBA3207 sp902797855	78.2978	86	391	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA3207	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 05:33:54,265] [INFO] GTDB search result was written to GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/result_gtdb.tsv
[2023-06-08 05:33:54,266] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:33:54,269] [INFO] DFAST_QC result json was written to GCA_902800935.1_Rumen_uncultured_genome_RUG14612_genomic.fna/dqc_result.json
[2023-06-08 05:33:54,269] [INFO] DFAST_QC completed!
[2023-06-08 05:33:54,269] [INFO] Total running time: 0h0m36s