[2023-06-05 00:30:32,248] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:30:32,255] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:30:32,255] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d10654b-7599-4e3c-84cd-3c3f0faffdf7/dqc_reference
[2023-06-05 00:30:33,855] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:30:33,856] [INFO] Task started: Prodigal
[2023-06-05 00:30:33,857] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ebf4659-0318-42af-95b7-517429bfa0b2/GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna.gz | prodigal -d GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/cds.fna -a GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:30:39,148] [INFO] Task succeeded: Prodigal
[2023-06-05 00:30:39,148] [INFO] Task started: HMMsearch
[2023-06-05 00:30:39,148] [INFO] Running command: hmmsearch --tblout GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d10654b-7599-4e3c-84cd-3c3f0faffdf7/dqc_reference/reference_markers.hmm GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:30:39,440] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:30:39,441] [INFO] Found 6/6 markers.
[2023-06-05 00:30:39,476] [INFO] Query marker FASTA was written to GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/markers.fasta
[2023-06-05 00:30:39,477] [INFO] Task started: Blastn
[2023-06-05 00:30:39,477] [INFO] Running command: blastn -query GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d10654b-7599-4e3c-84cd-3c3f0faffdf7/dqc_reference/reference_markers.fasta -out GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:30:40,066] [INFO] Task succeeded: Blastn
[2023-06-05 00:30:40,074] [INFO] Selected 24 target genomes.
[2023-06-05 00:30:40,075] [INFO] Target genome list was writen to GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/target_genomes.txt
[2023-06-05 00:30:40,077] [INFO] Task started: fastANI
[2023-06-05 00:30:40,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ebf4659-0318-42af-95b7-517429bfa0b2/GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna.gz --refList GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/target_genomes.txt --output GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:30:53,580] [INFO] Task succeeded: fastANI
[2023-06-05 00:30:53,580] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d10654b-7599-4e3c-84cd-3c3f0faffdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:30:53,581] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d10654b-7599-4e3c-84cd-3c3f0faffdf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:30:53,586] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:30:53,586] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 00:30:53,586] [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 flavefaciens	strain=ATCC 19208	GCA_000518765.1	1265	1265	suspected-type	True	79.1773	225	723	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.6005	67	723	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.4465	68	723	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 00:30:53,588] [INFO] DFAST Taxonomy check result was written to GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/tc_result.tsv
[2023-06-05 00:30:53,589] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:30:53,589] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:30:53,589] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d10654b-7599-4e3c-84cd-3c3f0faffdf7/dqc_reference/checkm_data
[2023-06-05 00:30:53,590] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:30:53,624] [INFO] Task started: CheckM
[2023-06-05 00:30:53,625] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/checkm_input GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/checkm_result
[2023-06-05 00:31:17,649] [INFO] Task succeeded: CheckM
[2023-06-05 00:31:17,651] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 81.25%
Contamintation: 1.39%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:31:17,675] [INFO] ===== Completeness check finished =====
[2023-06-05 00:31:17,676] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:31:17,676] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/markers.fasta)
[2023-06-05 00:31:17,677] [INFO] Task started: Blastn
[2023-06-05 00:31:17,677] [INFO] Running command: blastn -query GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d10654b-7599-4e3c-84cd-3c3f0faffdf7/dqc_reference/reference_markers_gtdb.fasta -out GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:31:18,455] [INFO] Task succeeded: Blastn
[2023-06-05 00:31:18,459] [INFO] Selected 15 target genomes.
[2023-06-05 00:31:18,459] [INFO] Target genome list was writen to GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:31:18,499] [INFO] Task started: fastANI
[2023-06-05 00:31:18,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ebf4659-0318-42af-95b7-517429bfa0b2/GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna.gz --refList GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/target_genomes_gtdb.txt --output GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:31:25,943] [INFO] Task succeeded: fastANI
[2023-06-05 00:31:25,969] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:31:25,969] [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_902762855.1	s__Ruminococcus flavefaciens_V	98.6971	606	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.58	98.43	0.85	0.84	3	conclusive
GCA_002371825.1	s__Ruminococcus flavefaciens_L	82.6337	371	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.29	98.12	0.89	0.86	3	-
GCA_001604035.1	s__Ruminococcus sp001604035	81.0944	319	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.76	98.76	0.77	0.77	2	-
GCA_012718885.1	s__Ruminococcus sp012718885	80.8108	303	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017441505.1	s__Ruminococcus sp017441505	79.6666	228	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900116855.1	s__Ruminococcus flavefaciens_R	79.5633	278	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.90	97.16	0.91	0.76	13	-
GCA_902777125.1	s__Ruminococcus sp900321885	79.4943	258	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	99.95	99.95	0.98	0.98	2	-
GCA_017543335.1	s__Ruminococcus sp017543335	79.4735	233	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.36	98.36	0.90	0.90	2	-
GCA_004556875.1	s__Ruminococcus flavefaciens_S	79.3079	151	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525915.1	s__Ruminococcus sp017525915	79.2061	247	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900108555.1	s__Ruminococcus flavefaciens_P	79.1299	237	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902780115.1	s__Ruminococcus flavefaciens_Y	79.0924	158	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017513795.1	s__Ruminococcus sp017513795	78.7065	148	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	97.92	97.92	0.90	0.90	2	-
GCF_000701945.1	s__Ruminococcus flavefaciens_B	78.6891	205	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	98.28	97.13	0.93	0.85	11	-
GCA_017479805.1	s__Ruminococcus sp017479805	78.4567	185	723	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:31:25,971] [INFO] GTDB search result was written to GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/result_gtdb.tsv
[2023-06-05 00:31:25,972] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:31:25,975] [INFO] DFAST_QC result json was written to GCA_902791565.1_Rumen_uncultured_genome_RUG13690_genomic.fna/dqc_result.json
[2023-06-05 00:31:25,975] [INFO] DFAST_QC completed!
[2023-06-05 00:31:25,975] [INFO] Total running time: 0h0m54s