[2023-06-05 09:37:03,355] [INFO] DFAST_QC pipeline started.
[2023-06-05 09:37:03,357] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 09:37:03,358] [INFO] DQC Reference Directory: /var/lib/cwl/stgc4d55b8f-cc0b-499a-b2db-7298b5e9d627/dqc_reference
[2023-06-05 09:37:04,704] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 09:37:04,705] [INFO] Task started: Prodigal
[2023-06-05 09:37:04,705] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ec9d42d-b46b-4de0-8d96-47e71f80310f/GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna.gz | prodigal -d GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/cds.fna -a GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 09:37:07,954] [INFO] Task succeeded: Prodigal
[2023-06-05 09:37:07,955] [INFO] Task started: HMMsearch
[2023-06-05 09:37:07,955] [INFO] Running command: hmmsearch --tblout GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc4d55b8f-cc0b-499a-b2db-7298b5e9d627/dqc_reference/reference_markers.hmm GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/protein.faa > /dev/null
[2023-06-05 09:37:08,208] [INFO] Task succeeded: HMMsearch
[2023-06-05 09:37:08,210] [INFO] Found 6/6 markers.
[2023-06-05 09:37:08,234] [INFO] Query marker FASTA was written to GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/markers.fasta
[2023-06-05 09:37:08,235] [INFO] Task started: Blastn
[2023-06-05 09:37:08,235] [INFO] Running command: blastn -query GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4d55b8f-cc0b-499a-b2db-7298b5e9d627/dqc_reference/reference_markers.fasta -out GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:37:08,930] [INFO] Task succeeded: Blastn
[2023-06-05 09:37:08,935] [INFO] Selected 14 target genomes.
[2023-06-05 09:37:08,935] [INFO] Target genome list was writen to GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/target_genomes.txt
[2023-06-05 09:37:08,939] [INFO] Task started: fastANI
[2023-06-05 09:37:08,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ec9d42d-b46b-4de0-8d96-47e71f80310f/GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna.gz --refList GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/target_genomes.txt --output GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 09:37:17,240] [INFO] Task succeeded: fastANI
[2023-06-05 09:37:17,240] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc4d55b8f-cc0b-499a-b2db-7298b5e9d627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 09:37:17,241] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc4d55b8f-cc0b-499a-b2db-7298b5e9d627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 09:37:17,245] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 09:37:17,245] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 09:37:17,246] [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	77.5672	62	438	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 09:37:17,248] [INFO] DFAST Taxonomy check result was written to GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/tc_result.tsv
[2023-06-05 09:37:17,249] [INFO] ===== Taxonomy check completed =====
[2023-06-05 09:37:17,249] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 09:37:17,250] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc4d55b8f-cc0b-499a-b2db-7298b5e9d627/dqc_reference/checkm_data
[2023-06-05 09:37:17,252] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 09:37:17,276] [INFO] Task started: CheckM
[2023-06-05 09:37:17,276] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/checkm_input GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/checkm_result
[2023-06-05 09:37:36,074] [INFO] Task succeeded: CheckM
[2023-06-05 09:37:36,075] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 86.55%
Contamintation: 4.17%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-05 09:37:36,098] [INFO] ===== Completeness check finished =====
[2023-06-05 09:37:36,099] [INFO] ===== Start GTDB Search =====
[2023-06-05 09:37:36,099] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/markers.fasta)
[2023-06-05 09:37:36,099] [INFO] Task started: Blastn
[2023-06-05 09:37:36,100] [INFO] Running command: blastn -query GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/markers.fasta -db /var/lib/cwl/stgc4d55b8f-cc0b-499a-b2db-7298b5e9d627/dqc_reference/reference_markers_gtdb.fasta -out GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 09:37:37,245] [INFO] Task succeeded: Blastn
[2023-06-05 09:37:37,249] [INFO] Selected 12 target genomes.
[2023-06-05 09:37:37,249] [INFO] Target genome list was writen to GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 09:37:37,252] [INFO] Task started: fastANI
[2023-06-05 09:37:37,252] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ec9d42d-b46b-4de0-8d96-47e71f80310f/GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna.gz --refList GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/target_genomes_gtdb.txt --output GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 09:37:41,928] [INFO] Task succeeded: fastANI
[2023-06-05 09:37:41,941] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 09:37:41,941] [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	99.3444	391	438	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	91.6269	197	438	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	88.2695	288	438	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	86.9014	354	438	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	81.9527	321	438	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_017471345.1	s__Ruminococcus_E sp017471345	80.4342	246	438	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_902761375.1	s__Ruminococcus_E sp902761375	79.978	206	438	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_900320415.1	s__Ruminococcus_E sp900320415	79.9389	197	438	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_902767845.1	s__Ruminococcus_E sp902767845	79.5491	202	438	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_017433905.1	s__Ruminococcus_E sp017433905	79.2532	132	438	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_900315085.1	s__Ruminococcus_E sp900315085	79.0366	189	438	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.46	97.96	0.77	0.69	11	-
GCA_900317315.1	s__Ruminococcus_E sp900317315	78.4686	189	438	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	98.84	97.27	0.87	0.80	119	-
--------------------------------------------------------------------------------
[2023-06-05 09:37:41,958] [INFO] GTDB search result was written to GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/result_gtdb.tsv
[2023-06-05 09:37:41,959] [INFO] ===== GTDB Search completed =====
[2023-06-05 09:37:41,963] [INFO] DFAST_QC result json was written to GCA_902784325.1_Rumen_uncultured_genome_RUG12960_genomic.fna/dqc_result.json
[2023-06-05 09:37:41,963] [INFO] DFAST_QC completed!
[2023-06-05 09:37:41,963] [INFO] Total running time: 0h0m39s