[2023-06-05 08:21:11,540] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:21:11,553] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:21:11,553] [INFO] DQC Reference Directory: /var/lib/cwl/stg47197fe9-e0ff-48e6-aebd-4409bf0c3b4b/dqc_reference
[2023-06-05 08:21:13,959] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:21:13,970] [INFO] Task started: Prodigal
[2023-06-05 08:21:13,970] [INFO] Running command: gunzip -c /var/lib/cwl/stg71da3ada-a089-4b8f-bfb3-3cea6d4968c7/GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna.gz | prodigal -d GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/cds.fna -a GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:21:16,111] [INFO] Task succeeded: Prodigal
[2023-06-05 08:21:16,112] [INFO] Task started: HMMsearch
[2023-06-05 08:21:16,112] [INFO] Running command: hmmsearch --tblout GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg47197fe9-e0ff-48e6-aebd-4409bf0c3b4b/dqc_reference/reference_markers.hmm GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:21:16,343] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:21:16,344] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg71da3ada-a089-4b8f-bfb3-3cea6d4968c7/GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna.gz]
[2023-06-05 08:21:16,361] [INFO] Query marker FASTA was written to GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/markers.fasta
[2023-06-05 08:21:16,362] [INFO] Task started: Blastn
[2023-06-05 08:21:16,362] [INFO] Running command: blastn -query GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/markers.fasta -db /var/lib/cwl/stg47197fe9-e0ff-48e6-aebd-4409bf0c3b4b/dqc_reference/reference_markers.fasta -out GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:21:16,944] [INFO] Task succeeded: Blastn
[2023-06-05 08:21:16,948] [INFO] Selected 20 target genomes.
[2023-06-05 08:21:16,948] [INFO] Target genome list was writen to GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/target_genomes.txt
[2023-06-05 08:21:16,952] [INFO] Task started: fastANI
[2023-06-05 08:21:16,952] [INFO] Running command: fastANI --query /var/lib/cwl/stg71da3ada-a089-4b8f-bfb3-3cea6d4968c7/GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna.gz --refList GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/target_genomes.txt --output GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:21:27,305] [INFO] Task succeeded: fastANI
[2023-06-05 08:21:27,306] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg47197fe9-e0ff-48e6-aebd-4409bf0c3b4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:21:27,306] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg47197fe9-e0ff-48e6-aebd-4409bf0c3b4b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:21:27,308] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:21:27,308] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 08:21:27,308] [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 08:21:27,310] [INFO] DFAST Taxonomy check result was written to GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/tc_result.tsv
[2023-06-05 08:21:27,311] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:21:27,311] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:21:27,311] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg47197fe9-e0ff-48e6-aebd-4409bf0c3b4b/dqc_reference/checkm_data
[2023-06-05 08:21:27,314] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:21:27,335] [INFO] Task started: CheckM
[2023-06-05 08:21:27,335] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/checkm_input GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/checkm_result
[2023-06-05 08:21:42,218] [INFO] Task succeeded: CheckM
[2023-06-05 08:21:42,219] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.73%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 08:21:42,247] [INFO] ===== Completeness check finished =====
[2023-06-05 08:21:42,248] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:21:42,248] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/markers.fasta)
[2023-06-05 08:21:42,249] [INFO] Task started: Blastn
[2023-06-05 08:21:42,249] [INFO] Running command: blastn -query GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/markers.fasta -db /var/lib/cwl/stg47197fe9-e0ff-48e6-aebd-4409bf0c3b4b/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:21:43,054] [INFO] Task succeeded: Blastn
[2023-06-05 08:21:43,058] [INFO] Selected 24 target genomes.
[2023-06-05 08:21:43,059] [INFO] Target genome list was writen to GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:21:43,098] [INFO] Task started: fastANI
[2023-06-05 08:21:43,098] [INFO] Running command: fastANI --query /var/lib/cwl/stg71da3ada-a089-4b8f-bfb3-3cea6d4968c7/GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna.gz --refList GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/target_genomes_gtdb.txt --output GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:21:51,763] [INFO] Task succeeded: fastANI
[2023-06-05 08:21:51,770] [INFO] Found 3 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:21:51,770] [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_902784015.1	s__Bulleidia sp902784015	100.0	331	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_902766675.1	s__Bulleidia sp902766675	77.5154	70	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017475415.1	s__Bulleidia sp017475415	77.2881	55	338	d__Bacteria;p__Firmicutes;c__Bacilli;o__Erysipelotrichales;f__Erysipelotrichaceae;g__Bulleidia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 08:21:51,772] [INFO] GTDB search result was written to GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/result_gtdb.tsv
[2023-06-05 08:21:51,772] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:21:51,779] [INFO] DFAST_QC result json was written to GCA_902784015.1_Rumen_uncultured_genome_RUG12927_genomic.fna/dqc_result.json
[2023-06-05 08:21:51,779] [INFO] DFAST_QC completed!
[2023-06-05 08:21:51,779] [INFO] Total running time: 0h0m40s