[2023-06-05 15:05:29,954] [INFO] DFAST_QC pipeline started.
[2023-06-05 15:05:29,974] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 15:05:29,975] [INFO] DQC Reference Directory: /var/lib/cwl/stgf6f58d2f-6e74-4e40-9b9a-2328cbb1dd36/dqc_reference
[2023-06-05 15:05:31,302] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 15:05:31,303] [INFO] Task started: Prodigal
[2023-06-05 15:05:31,303] [INFO] Running command: gunzip -c /var/lib/cwl/stg23f16894-8e36-43df-a4ad-c8e0a87857da/GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna.gz | prodigal -d GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/cds.fna -a GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 15:05:34,408] [INFO] Task succeeded: Prodigal
[2023-06-05 15:05:34,408] [INFO] Task started: HMMsearch
[2023-06-05 15:05:34,408] [INFO] Running command: hmmsearch --tblout GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf6f58d2f-6e74-4e40-9b9a-2328cbb1dd36/dqc_reference/reference_markers.hmm GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/protein.faa > /dev/null
[2023-06-05 15:05:34,587] [INFO] Task succeeded: HMMsearch
[2023-06-05 15:05:34,588] [INFO] Found 6/6 markers.
[2023-06-05 15:05:34,608] [INFO] Query marker FASTA was written to GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/markers.fasta
[2023-06-05 15:05:34,608] [INFO] Task started: Blastn
[2023-06-05 15:05:34,608] [INFO] Running command: blastn -query GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6f58d2f-6e74-4e40-9b9a-2328cbb1dd36/dqc_reference/reference_markers.fasta -out GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:05:35,252] [INFO] Task succeeded: Blastn
[2023-06-05 15:05:35,256] [INFO] Selected 18 target genomes.
[2023-06-05 15:05:35,256] [INFO] Target genome list was writen to GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/target_genomes.txt
[2023-06-05 15:05:35,259] [INFO] Task started: fastANI
[2023-06-05 15:05:35,259] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f16894-8e36-43df-a4ad-c8e0a87857da/GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna.gz --refList GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/target_genomes.txt --output GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 15:05:46,479] [INFO] Task succeeded: fastANI
[2023-06-05 15:05:46,479] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf6f58d2f-6e74-4e40-9b9a-2328cbb1dd36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 15:05:46,480] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf6f58d2f-6e74-4e40-9b9a-2328cbb1dd36/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 15:05:46,483] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 15:05:46,484] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 15:05:46,484] [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
Ruminococcus bromii	strain=ATCC 27255	GCA_002834225.1	40518	40518	suspected-type	True	77.4734	63	393	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 15:05:46,486] [INFO] DFAST Taxonomy check result was written to GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/tc_result.tsv
[2023-06-05 15:05:46,487] [INFO] ===== Taxonomy check completed =====
[2023-06-05 15:05:46,487] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 15:05:46,487] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf6f58d2f-6e74-4e40-9b9a-2328cbb1dd36/dqc_reference/checkm_data
[2023-06-05 15:05:46,488] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 15:05:46,508] [INFO] Task started: CheckM
[2023-06-05 15:05:46,509] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/checkm_input GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/checkm_result
[2023-06-05 15:06:02,585] [INFO] Task succeeded: CheckM
[2023-06-05 15:06:02,586] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 93.79%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 15:06:02,608] [INFO] ===== Completeness check finished =====
[2023-06-05 15:06:02,609] [INFO] ===== Start GTDB Search =====
[2023-06-05 15:06:02,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/markers.fasta)
[2023-06-05 15:06:02,609] [INFO] Task started: Blastn
[2023-06-05 15:06:02,609] [INFO] Running command: blastn -query GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/markers.fasta -db /var/lib/cwl/stgf6f58d2f-6e74-4e40-9b9a-2328cbb1dd36/dqc_reference/reference_markers_gtdb.fasta -out GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 15:06:03,711] [INFO] Task succeeded: Blastn
[2023-06-05 15:06:03,716] [INFO] Selected 11 target genomes.
[2023-06-05 15:06:03,716] [INFO] Target genome list was writen to GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 15:06:03,722] [INFO] Task started: fastANI
[2023-06-05 15:06:03,722] [INFO] Running command: fastANI --query /var/lib/cwl/stg23f16894-8e36-43df-a4ad-c8e0a87857da/GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna.gz --refList GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/target_genomes_gtdb.txt --output GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 15:06:08,287] [INFO] Task succeeded: fastANI
[2023-06-05 15:06:08,297] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 15:06:08,298] [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_900316555.1	s__Ruminococcus_E sp900316555	99.2863	355	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.80	96.62	0.88	0.77	62	conclusive
GCF_016680995.1	s__Ruminococcus_E sp016680995	91.7362	174	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018918205.1	s__Ruminococcus_E sp018918205	87.739	257	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765625.1	s__Ruminococcus_E sp902765625	86.601	316	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.31	99.27	0.90	0.89	5	-
GCA_900100595.1	s__Ruminococcus_E sp900100595	81.7346	265	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.87	97.87	0.91	0.78	34	-
GCA_900320415.1	s__Ruminococcus_E sp900320415	80.0129	170	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.69	99.69	0.84	0.84	2	-
GCA_017471345.1	s__Ruminococcus_E sp017471345	79.7695	223	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902767845.1	s__Ruminococcus_E sp902767845	79.7058	177	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.96	98.96	0.86	0.86	2	-
GCA_902776375.1	s__Ruminococcus_E sp902776375	79.4498	184	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902784855.1	s__Ruminococcus_E sp902784855	79.345	186	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017433905.1	s__Ruminococcus_E sp017433905	78.9925	113	393	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 15:06:08,300] [INFO] GTDB search result was written to GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/result_gtdb.tsv
[2023-06-05 15:06:08,302] [INFO] ===== GTDB Search completed =====
[2023-06-05 15:06:08,306] [INFO] DFAST_QC result json was written to GCA_902761085.1_Rumen_uncultured_genome_RUG10630_genomic.fna/dqc_result.json
[2023-06-05 15:06:08,306] [INFO] DFAST_QC completed!
[2023-06-05 15:06:08,306] [INFO] Total running time: 0h0m38s