[2023-06-08 11:15:59,822] [INFO] DFAST_QC pipeline started.
[2023-06-08 11:15:59,824] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 11:15:59,824] [INFO] DQC Reference Directory: /var/lib/cwl/stge00fdbce-fc64-4815-a110-510366debbc8/dqc_reference
[2023-06-08 11:16:01,048] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 11:16:01,049] [INFO] Task started: Prodigal
[2023-06-08 11:16:01,049] [INFO] Running command: gunzip -c /var/lib/cwl/stg7dbaf6b7-3c0e-41c1-8ba5-ff95f5ee136b/GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna.gz | prodigal -d GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/cds.fna -a GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 11:16:07,146] [INFO] Task succeeded: Prodigal
[2023-06-08 11:16:07,147] [INFO] Task started: HMMsearch
[2023-06-08 11:16:07,147] [INFO] Running command: hmmsearch --tblout GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge00fdbce-fc64-4815-a110-510366debbc8/dqc_reference/reference_markers.hmm GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/protein.faa > /dev/null
[2023-06-08 11:16:07,458] [INFO] Task succeeded: HMMsearch
[2023-06-08 11:16:07,460] [INFO] Found 6/6 markers.
[2023-06-08 11:16:07,493] [INFO] Query marker FASTA was written to GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/markers.fasta
[2023-06-08 11:16:07,494] [INFO] Task started: Blastn
[2023-06-08 11:16:07,494] [INFO] Running command: blastn -query GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/markers.fasta -db /var/lib/cwl/stge00fdbce-fc64-4815-a110-510366debbc8/dqc_reference/reference_markers.fasta -out GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:08,110] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:08,114] [INFO] Selected 14 target genomes.
[2023-06-08 11:16:08,114] [INFO] Target genome list was writen to GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/target_genomes.txt
[2023-06-08 11:16:08,116] [INFO] Task started: fastANI
[2023-06-08 11:16:08,117] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dbaf6b7-3c0e-41c1-8ba5-ff95f5ee136b/GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna.gz --refList GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/target_genomes.txt --output GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 11:16:19,342] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:19,342] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge00fdbce-fc64-4815-a110-510366debbc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 11:16:19,343] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge00fdbce-fc64-4815-a110-510366debbc8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 11:16:19,348] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 11:16:19,348] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 11:16:19,348] [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 bicirculans	strain=80/3	GCA_000723465.1	1160721	1160721	type	True	77.9736	113	797	95	below_threshold
Ruminococcus albus	strain=DSM 20455	GCA_000621285.1	1264	1264	suspected-type	True	77.9285	130	797	95	below_threshold
Ruminococcus albus	strain=7	GCA_000179635.2	1264	1264	suspected-type	True	77.9065	129	797	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 11:16:19,350] [INFO] DFAST Taxonomy check result was written to GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/tc_result.tsv
[2023-06-08 11:16:19,351] [INFO] ===== Taxonomy check completed =====
[2023-06-08 11:16:19,351] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 11:16:19,352] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge00fdbce-fc64-4815-a110-510366debbc8/dqc_reference/checkm_data
[2023-06-08 11:16:19,353] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 11:16:19,389] [INFO] Task started: CheckM
[2023-06-08 11:16:19,389] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/checkm_input GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/checkm_result
[2023-06-08 11:16:45,282] [INFO] Task succeeded: CheckM
[2023-06-08 11:16:45,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 80.64%
Contamintation: 15.10%
Strain heterogeneity: 14.29%
--------------------------------------------------------------------------------
[2023-06-08 11:16:45,310] [INFO] ===== Completeness check finished =====
[2023-06-08 11:16:45,311] [INFO] ===== Start GTDB Search =====
[2023-06-08 11:16:45,311] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/markers.fasta)
[2023-06-08 11:16:45,311] [INFO] Task started: Blastn
[2023-06-08 11:16:45,312] [INFO] Running command: blastn -query GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/markers.fasta -db /var/lib/cwl/stge00fdbce-fc64-4815-a110-510366debbc8/dqc_reference/reference_markers_gtdb.fasta -out GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 11:16:46,201] [INFO] Task succeeded: Blastn
[2023-06-08 11:16:46,206] [INFO] Selected 14 target genomes.
[2023-06-08 11:16:46,206] [INFO] Target genome list was writen to GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 11:16:46,210] [INFO] Task started: fastANI
[2023-06-08 11:16:46,210] [INFO] Running command: fastANI --query /var/lib/cwl/stg7dbaf6b7-3c0e-41c1-8ba5-ff95f5ee136b/GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna.gz --refList GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/target_genomes_gtdb.txt --output GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 11:16:53,304] [INFO] Task succeeded: fastANI
[2023-06-08 11:16:53,324] [INFO] Found 11 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-08 11:16:53,325] [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_900314975.1	s__Ruminococcus_D sp900314975	81.5085	442	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.52	97.44	0.93	0.89	4	-
GCA_902786965.1	s__Ruminococcus_D sp902786965	81.1606	415	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.48	97.28	0.83	0.79	5	-
GCA_902786975.1	s__Ruminococcus_D sp902786975	80.6927	379	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.61	98.61	0.94	0.94	2	-
GCA_902787825.1	s__Ruminococcus_D sp902787825	80.5143	386	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002371625.1	s__Ruminococcus_D sp002371625	80.0298	269	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	98.14	97.32	0.90	0.85	5	-
GCF_000621805.1	s__Ruminococcus_D sp000621805	79.8735	298	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000178155.2	s__Ruminococcus_D albus_C	77.8111	117	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.72	97.29	0.89	0.84	5	-
GCA_902762735.1	s__Ruminococcus_D sp902762735	77.7546	127	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.61	97.61	0.90	0.90	2	-
GCA_017464355.1	s__Ruminococcus_D sp017464355	77.7111	104	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017438745.1	s__HUN007 sp017438745	76.3845	55	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__HUN007	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902797535.1	s__Ruminococcus_D sp902797535	76.0571	73	797	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Ruminococcaceae;g__Ruminococcus_D	95.0	97.84	97.84	0.78	0.78	2	-
--------------------------------------------------------------------------------
[2023-06-08 11:16:53,327] [INFO] GTDB search result was written to GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/result_gtdb.tsv
[2023-06-08 11:16:53,327] [INFO] ===== GTDB Search completed =====
[2023-06-08 11:16:53,330] [INFO] DFAST_QC result json was written to GCA_902787285.1_Rumen_uncultured_genome_RUG13258_genomic.fna/dqc_result.json
[2023-06-08 11:16:53,330] [INFO] DFAST_QC completed!
[2023-06-08 11:16:53,330] [INFO] Total running time: 0h0m54s