[2023-06-05 06:18:29,723] [INFO] DFAST_QC pipeline started.
[2023-06-05 06:18:29,725] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 06:18:29,725] [INFO] DQC Reference Directory: /var/lib/cwl/stg47145372-df70-432a-a7b4-004dbadf181f/dqc_reference
[2023-06-05 06:18:30,919] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 06:18:30,920] [INFO] Task started: Prodigal
[2023-06-05 06:18:30,920] [INFO] Running command: gunzip -c /var/lib/cwl/stg908420cd-4272-4c9c-b8d3-a4bdf5dc5c61/GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna.gz | prodigal -d GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/cds.fna -a GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 06:18:35,041] [INFO] Task succeeded: Prodigal
[2023-06-05 06:18:35,041] [INFO] Task started: HMMsearch
[2023-06-05 06:18:35,041] [INFO] Running command: hmmsearch --tblout GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47145372-df70-432a-a7b4-004dbadf181f/dqc_reference/reference_markers.hmm GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/protein.faa > /dev/null
[2023-06-05 06:18:35,234] [INFO] Task succeeded: HMMsearch
[2023-06-05 06:18:35,235] [INFO] Found 6/6 markers.
[2023-06-05 06:18:35,255] [INFO] Query marker FASTA was written to GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/markers.fasta
[2023-06-05 06:18:35,255] [INFO] Task started: Blastn
[2023-06-05 06:18:35,255] [INFO] Running command: blastn -query GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/markers.fasta -db /var/lib/cwl/stg47145372-df70-432a-a7b4-004dbadf181f/dqc_reference/reference_markers.fasta -out GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:18:35,842] [INFO] Task succeeded: Blastn
[2023-06-05 06:18:35,846] [INFO] Selected 20 target genomes.
[2023-06-05 06:18:35,846] [INFO] Target genome list was writen to GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/target_genomes.txt
[2023-06-05 06:18:35,851] [INFO] Task started: fastANI
[2023-06-05 06:18:35,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg908420cd-4272-4c9c-b8d3-a4bdf5dc5c61/GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna.gz --refList GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/target_genomes.txt --output GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 06:18:44,815] [INFO] Task succeeded: fastANI
[2023-06-05 06:18:44,815] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47145372-df70-432a-a7b4-004dbadf181f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 06:18:44,816] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47145372-df70-432a-a7b4-004dbadf181f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 06:18:44,817] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 06:18:44,817] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 06:18:44,817] [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 06:18:44,819] [INFO] DFAST Taxonomy check result was written to GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/tc_result.tsv
[2023-06-05 06:18:44,819] [INFO] ===== Taxonomy check completed =====
[2023-06-05 06:18:44,819] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 06:18:44,820] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47145372-df70-432a-a7b4-004dbadf181f/dqc_reference/checkm_data
[2023-06-05 06:18:44,822] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 06:18:44,845] [INFO] Task started: CheckM
[2023-06-05 06:18:44,845] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/checkm_input GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/checkm_result
[2023-06-05 06:19:04,393] [INFO] Task succeeded: CheckM
[2023-06-05 06:19:04,394] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 06:19:04,411] [INFO] ===== Completeness check finished =====
[2023-06-05 06:19:04,411] [INFO] ===== Start GTDB Search =====
[2023-06-05 06:19:04,411] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/markers.fasta)
[2023-06-05 06:19:04,412] [INFO] Task started: Blastn
[2023-06-05 06:19:04,412] [INFO] Running command: blastn -query GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/markers.fasta -db /var/lib/cwl/stg47145372-df70-432a-a7b4-004dbadf181f/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 06:19:05,396] [INFO] Task succeeded: Blastn
[2023-06-05 06:19:05,399] [INFO] Selected 16 target genomes.
[2023-06-05 06:19:05,399] [INFO] Target genome list was writen to GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 06:19:05,406] [INFO] Task started: fastANI
[2023-06-05 06:19:05,406] [INFO] Running command: fastANI --query /var/lib/cwl/stg908420cd-4272-4c9c-b8d3-a4bdf5dc5c61/GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna.gz --refList GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/target_genomes_gtdb.txt --output GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 06:19:11,926] [INFO] Task succeeded: fastANI
[2023-06-05 06:19:11,932] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 06:19:11,933] [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_902772795.1	s__CAG-964 sp902772795	97.5695	330	468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-964	95.0	97.62	97.62	0.71	0.71	2	conclusive
GCA_902762375.1	s__CAG-964 sp902762375	80.8593	293	468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902773265.1	s__CAG-964 sp902773265	80.1512	179	468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-964	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900316025.1	s__CAG-964 sp900316025	76.6427	89	468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-964	95.0	99.29	99.19	0.92	0.90	5	-
GCA_900316615.1	s__CAG-964 sp900316615	76.4012	63	468	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__CAG-964	95.0	99.04	98.75	0.90	0.87	13	-
--------------------------------------------------------------------------------
[2023-06-05 06:19:11,949] [INFO] GTDB search result was written to GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/result_gtdb.tsv
[2023-06-05 06:19:11,950] [INFO] ===== GTDB Search completed =====
[2023-06-05 06:19:11,954] [INFO] DFAST_QC result json was written to GCA_902767185.1_Rumen_uncultured_genome_RUG11235_genomic.fna/dqc_result.json
[2023-06-05 06:19:11,954] [INFO] DFAST_QC completed!
[2023-06-05 06:19:11,954] [INFO] Total running time: 0h0m42s