[2023-06-08 09:17:38,369] [INFO] DFAST_QC pipeline started.
[2023-06-08 09:17:38,372] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 09:17:38,372] [INFO] DQC Reference Directory: /var/lib/cwl/stgd2eeee8a-ded3-4799-be92-e7ddcfd2add3/dqc_reference
[2023-06-08 09:17:39,726] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 09:17:39,727] [INFO] Task started: Prodigal
[2023-06-08 09:17:39,727] [INFO] Running command: gunzip -c /var/lib/cwl/stgf960d41d-a6cf-4038-ac9c-2011a7cc9a0b/GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna.gz | prodigal -d GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/cds.fna -a GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 09:17:41,595] [INFO] Task succeeded: Prodigal
[2023-06-08 09:17:41,595] [INFO] Task started: HMMsearch
[2023-06-08 09:17:41,595] [INFO] Running command: hmmsearch --tblout GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd2eeee8a-ded3-4799-be92-e7ddcfd2add3/dqc_reference/reference_markers.hmm GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/protein.faa > /dev/null
[2023-06-08 09:17:41,863] [INFO] Task succeeded: HMMsearch
[2023-06-08 09:17:41,864] [INFO] Found 6/6 markers.
[2023-06-08 09:17:41,881] [INFO] Query marker FASTA was written to GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/markers.fasta
[2023-06-08 09:17:41,882] [INFO] Task started: Blastn
[2023-06-08 09:17:41,882] [INFO] Running command: blastn -query GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2eeee8a-ded3-4799-be92-e7ddcfd2add3/dqc_reference/reference_markers.fasta -out GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:17:42,637] [INFO] Task succeeded: Blastn
[2023-06-08 09:17:42,656] [INFO] Selected 20 target genomes.
[2023-06-08 09:17:42,657] [INFO] Target genome list was writen to GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/target_genomes.txt
[2023-06-08 09:17:42,661] [INFO] Task started: fastANI
[2023-06-08 09:17:42,662] [INFO] Running command: fastANI --query /var/lib/cwl/stgf960d41d-a6cf-4038-ac9c-2011a7cc9a0b/GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna.gz --refList GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/target_genomes.txt --output GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 09:17:51,430] [INFO] Task succeeded: fastANI
[2023-06-08 09:17:51,431] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd2eeee8a-ded3-4799-be92-e7ddcfd2add3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 09:17:51,431] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd2eeee8a-ded3-4799-be92-e7ddcfd2add3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 09:17:51,434] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 09:17:51,434] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 09:17:51,434] [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 09:17:51,437] [INFO] DFAST Taxonomy check result was written to GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/tc_result.tsv
[2023-06-08 09:17:51,437] [INFO] ===== Taxonomy check completed =====
[2023-06-08 09:17:51,438] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 09:17:51,438] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd2eeee8a-ded3-4799-be92-e7ddcfd2add3/dqc_reference/checkm_data
[2023-06-08 09:17:51,443] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 09:17:51,460] [INFO] Task started: CheckM
[2023-06-08 09:17:51,461] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/checkm_input GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/checkm_result
[2023-06-08 09:18:06,004] [INFO] Task succeeded: CheckM
[2023-06-08 09:18:06,006] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.46%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 09:18:06,027] [INFO] ===== Completeness check finished =====
[2023-06-08 09:18:06,028] [INFO] ===== Start GTDB Search =====
[2023-06-08 09:18:06,028] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/markers.fasta)
[2023-06-08 09:18:06,028] [INFO] Task started: Blastn
[2023-06-08 09:18:06,029] [INFO] Running command: blastn -query GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/markers.fasta -db /var/lib/cwl/stgd2eeee8a-ded3-4799-be92-e7ddcfd2add3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 09:18:06,986] [INFO] Task succeeded: Blastn
[2023-06-08 09:18:06,996] [INFO] Selected 20 target genomes.
[2023-06-08 09:18:06,996] [INFO] Target genome list was writen to GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 09:18:07,008] [INFO] Task started: fastANI
[2023-06-08 09:18:07,009] [INFO] Running command: fastANI --query /var/lib/cwl/stgf960d41d-a6cf-4038-ac9c-2011a7cc9a0b/GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna.gz --refList GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/target_genomes_gtdb.txt --output GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 09:18:11,786] [INFO] Task succeeded: fastANI
[2023-06-08 09:18:11,791] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 09:18:11,791] [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_902796285.1	s__Caccovivens sp902796285	100.0	255	257	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900557645.1	s__Caccovivens sp900557645	78.2709	60	257	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	99.83	99.83	0.95	0.95	2	-
GCA_017621525.1	s__Caccovivens sp017621525	77.2218	50	257	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__UBA1242;g__Caccovivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 09:18:11,793] [INFO] GTDB search result was written to GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/result_gtdb.tsv
[2023-06-08 09:18:11,793] [INFO] ===== GTDB Search completed =====
[2023-06-08 09:18:11,796] [INFO] DFAST_QC result json was written to GCA_902796285.1_Rumen_uncultured_genome_RUG14149_genomic.fna/dqc_result.json
[2023-06-08 09:18:11,796] [INFO] DFAST_QC completed!
[2023-06-08 09:18:11,796] [INFO] Total running time: 0h0m33s