[2023-06-08 05:33:40,127] [INFO] DFAST_QC pipeline started.
[2023-06-08 05:33:40,129] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 05:33:40,130] [INFO] DQC Reference Directory: /var/lib/cwl/stgd80817f3-7b42-4a8b-ade4-ac7d0ef69859/dqc_reference
[2023-06-08 05:33:41,554] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 05:33:41,555] [INFO] Task started: Prodigal
[2023-06-08 05:33:41,555] [INFO] Running command: gunzip -c /var/lib/cwl/stg68c0f4fb-c403-4395-ad94-3ba0b842554a/GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna.gz | prodigal -d GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/cds.fna -a GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 05:33:48,047] [INFO] Task succeeded: Prodigal
[2023-06-08 05:33:48,048] [INFO] Task started: HMMsearch
[2023-06-08 05:33:48,048] [INFO] Running command: hmmsearch --tblout GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd80817f3-7b42-4a8b-ade4-ac7d0ef69859/dqc_reference/reference_markers.hmm GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/protein.faa > /dev/null
[2023-06-08 05:33:48,333] [INFO] Task succeeded: HMMsearch
[2023-06-08 05:33:48,334] [INFO] Found 6/6 markers.
[2023-06-08 05:33:48,357] [INFO] Query marker FASTA was written to GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/markers.fasta
[2023-06-08 05:33:48,358] [INFO] Task started: Blastn
[2023-06-08 05:33:48,358] [INFO] Running command: blastn -query GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/markers.fasta -db /var/lib/cwl/stgd80817f3-7b42-4a8b-ade4-ac7d0ef69859/dqc_reference/reference_markers.fasta -out GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:33:49,035] [INFO] Task succeeded: Blastn
[2023-06-08 05:33:49,039] [INFO] Selected 27 target genomes.
[2023-06-08 05:33:49,039] [INFO] Target genome list was writen to GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/target_genomes.txt
[2023-06-08 05:33:49,041] [INFO] Task started: fastANI
[2023-06-08 05:33:49,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c0f4fb-c403-4395-ad94-3ba0b842554a/GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna.gz --refList GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/target_genomes.txt --output GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 05:34:06,749] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:06,750] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd80817f3-7b42-4a8b-ade4-ac7d0ef69859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 05:34:06,750] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd80817f3-7b42-4a8b-ade4-ac7d0ef69859/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 05:34:06,754] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 05:34:06,754] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 05:34:06,754] [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	76.6962	60	720	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 05:34:06,757] [INFO] DFAST Taxonomy check result was written to GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/tc_result.tsv
[2023-06-08 05:34:06,757] [INFO] ===== Taxonomy check completed =====
[2023-06-08 05:34:06,757] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 05:34:06,758] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd80817f3-7b42-4a8b-ade4-ac7d0ef69859/dqc_reference/checkm_data
[2023-06-08 05:34:06,759] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 05:34:06,786] [INFO] Task started: CheckM
[2023-06-08 05:34:06,786] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/checkm_input GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/checkm_result
[2023-06-08 05:34:31,535] [INFO] Task succeeded: CheckM
[2023-06-08 05:34:31,537] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.31%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 05:34:31,564] [INFO] ===== Completeness check finished =====
[2023-06-08 05:34:31,565] [INFO] ===== Start GTDB Search =====
[2023-06-08 05:34:31,565] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/markers.fasta)
[2023-06-08 05:34:31,566] [INFO] Task started: Blastn
[2023-06-08 05:34:31,566] [INFO] Running command: blastn -query GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/markers.fasta -db /var/lib/cwl/stgd80817f3-7b42-4a8b-ade4-ac7d0ef69859/dqc_reference/reference_markers_gtdb.fasta -out GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 05:34:32,735] [INFO] Task succeeded: Blastn
[2023-06-08 05:34:32,739] [INFO] Selected 12 target genomes.
[2023-06-08 05:34:32,740] [INFO] Target genome list was writen to GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 05:34:32,742] [INFO] Task started: fastANI
[2023-06-08 05:34:32,742] [INFO] Running command: fastANI --query /var/lib/cwl/stg68c0f4fb-c403-4395-ad94-3ba0b842554a/GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna.gz --refList GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/target_genomes_gtdb.txt --output GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 05:34:38,803] [INFO] Task succeeded: fastANI
[2023-06-08 05:34:38,817] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 05:34:38,818] [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_900317315.1	s__Ruminococcus_E sp900317315	97.3228	506	720	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	conclusive
GCA_902784855.1	s__Ruminococcus_E sp902784855	82.0789	401	720	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_900316815.1	s__Ruminococcus_E sp900316815	81.8511	340	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.08	98.49	0.85	0.78	7	-
GCA_902799325.1	s__Ruminococcus_E sp902799325	81.7638	351	720	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_902794395.1	s__Ruminococcus_E sp902794395	80.5769	387	720	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_900317595.1	s__Ruminococcus_E sp900317595	80.3837	310	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.55	99.10	0.91	0.83	3	-
GCA_902776375.1	s__Ruminococcus_E sp902776375	80.3582	392	720	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_900100595.1	s__Ruminococcus_E sp900100595	80.1603	332	720	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_902797525.1	s__Ruminococcus_E sp902797525	79.9663	266	720	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_900315195.1	s__Ruminococcus_E sp900315195	79.0505	261	720	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Ruminococcus_E	95.0	99.59	99.19	0.95	0.90	3	-
GCA_900320415.1	s__Ruminococcus_E sp900320415	79.0247	189	720	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_900316555.1	s__Ruminococcus_E sp900316555	79.0165	242	720	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	-
--------------------------------------------------------------------------------
[2023-06-08 05:34:38,820] [INFO] GTDB search result was written to GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/result_gtdb.tsv
[2023-06-08 05:34:38,820] [INFO] ===== GTDB Search completed =====
[2023-06-08 05:34:38,823] [INFO] DFAST_QC result json was written to GCA_902779175.1_Rumen_uncultured_genome_RUG12443_genomic.fna/dqc_result.json
[2023-06-08 05:34:38,823] [INFO] DFAST_QC completed!
[2023-06-08 05:34:38,824] [INFO] Total running time: 0h0m59s