[2023-06-05 23:13:56,883] [INFO] DFAST_QC pipeline started.
[2023-06-05 23:13:56,885] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 23:13:56,885] [INFO] DQC Reference Directory: /var/lib/cwl/stgec94f2a7-c5a2-4f81-a418-d36c636a8aef/dqc_reference
[2023-06-05 23:13:57,993] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 23:13:57,994] [INFO] Task started: Prodigal
[2023-06-05 23:13:57,994] [INFO] Running command: gunzip -c /var/lib/cwl/stg31ecff6e-b74c-43ba-8fc0-49c7ca1cb776/GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna.gz | prodigal -d GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/cds.fna -a GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 23:14:02,721] [INFO] Task succeeded: Prodigal
[2023-06-05 23:14:02,721] [INFO] Task started: HMMsearch
[2023-06-05 23:14:02,721] [INFO] Running command: hmmsearch --tblout GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgec94f2a7-c5a2-4f81-a418-d36c636a8aef/dqc_reference/reference_markers.hmm GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/protein.faa > /dev/null
[2023-06-05 23:14:02,885] [INFO] Task succeeded: HMMsearch
[2023-06-05 23:14:02,886] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg31ecff6e-b74c-43ba-8fc0-49c7ca1cb776/GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna.gz]
[2023-06-05 23:14:02,908] [INFO] Query marker FASTA was written to GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/markers.fasta
[2023-06-05 23:14:02,908] [INFO] Task started: Blastn
[2023-06-05 23:14:02,908] [INFO] Running command: blastn -query GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/markers.fasta -db /var/lib/cwl/stgec94f2a7-c5a2-4f81-a418-d36c636a8aef/dqc_reference/reference_markers.fasta -out GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:14:03,492] [INFO] Task succeeded: Blastn
[2023-06-05 23:14:03,495] [INFO] Selected 21 target genomes.
[2023-06-05 23:14:03,495] [INFO] Target genome list was writen to GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/target_genomes.txt
[2023-06-05 23:14:03,503] [INFO] Task started: fastANI
[2023-06-05 23:14:03,503] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ecff6e-b74c-43ba-8fc0-49c7ca1cb776/GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna.gz --refList GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/target_genomes.txt --output GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 23:14:13,962] [INFO] Task succeeded: fastANI
[2023-06-05 23:14:13,962] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgec94f2a7-c5a2-4f81-a418-d36c636a8aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 23:14:13,963] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgec94f2a7-c5a2-4f81-a418-d36c636a8aef/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 23:14:13,964] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 23:14:13,964] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 23:14:13,964] [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
--------------------------------------------------------------------------------
[2023-06-05 23:14:13,966] [INFO] DFAST Taxonomy check result was written to GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/tc_result.tsv
[2023-06-05 23:14:13,966] [INFO] ===== Taxonomy check completed =====
[2023-06-05 23:14:13,966] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 23:14:13,967] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgec94f2a7-c5a2-4f81-a418-d36c636a8aef/dqc_reference/checkm_data
[2023-06-05 23:14:13,969] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 23:14:13,993] [INFO] Task started: CheckM
[2023-06-05 23:14:13,993] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/checkm_input GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/checkm_result
[2023-06-05 23:14:32,704] [INFO] Task succeeded: CheckM
[2023-06-05 23:14:32,705] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 82.95%
Contamintation: 15.51%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2023-06-05 23:14:32,722] [INFO] ===== Completeness check finished =====
[2023-06-05 23:14:32,722] [INFO] ===== Start GTDB Search =====
[2023-06-05 23:14:32,722] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/markers.fasta)
[2023-06-05 23:14:32,723] [INFO] Task started: Blastn
[2023-06-05 23:14:32,723] [INFO] Running command: blastn -query GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/markers.fasta -db /var/lib/cwl/stgec94f2a7-c5a2-4f81-a418-d36c636a8aef/dqc_reference/reference_markers_gtdb.fasta -out GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 23:14:33,727] [INFO] Task succeeded: Blastn
[2023-06-05 23:14:33,730] [INFO] Selected 10 target genomes.
[2023-06-05 23:14:33,730] [INFO] Target genome list was writen to GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 23:14:33,736] [INFO] Task started: fastANI
[2023-06-05 23:14:33,736] [INFO] Running command: fastANI --query /var/lib/cwl/stg31ecff6e-b74c-43ba-8fc0-49c7ca1cb776/GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna.gz --refList GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/target_genomes_gtdb.txt --output GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 23:14:38,647] [INFO] Task succeeded: fastANI
[2023-06-05 23:14:38,654] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 23:14:38,654] [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_902768995.1	s__RUG472 sp902768995	98.2348	347	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	98.42	98.10	0.83	0.75	15	conclusive
GCA_900319345.1	s__RUG472 sp900319345	94.8544	407	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	98.47	97.84	0.91	0.80	6	-
GCA_902786465.1	s__RUG472 sp902786465	93.7235	384	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.79	0.84	0.84	2	-
GCA_902761365.1	s__RUG472 sp902761365	87.4013	386	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902802805.1	s__RUG472 sp902802805	87.2225	361	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	97.22	97.22	0.86	0.86	2	-
GCA_902801845.1	s__RUG472 sp902801845	86.6576	409	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	96.79	96.35	0.92	0.91	4	-
GCA_902802575.1	s__RUG472 sp902802575	86.6208	367	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	95.40	95.40	0.82	0.82	2	-
GCA_902798825.1	s__RUG472 sp902798825	86.3422	378	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	97.85	97.83	0.89	0.89	3	-
GCA_017545535.1	s__RUG472 sp017545535	86.1081	396	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902765005.1	s__RUG472 sp902765005	85.1385	387	505	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Christensenellales;f__CAG-138;g__RUG472	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 23:14:38,656] [INFO] GTDB search result was written to GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/result_gtdb.tsv
[2023-06-05 23:14:38,656] [INFO] ===== GTDB Search completed =====
[2023-06-05 23:14:38,658] [INFO] DFAST_QC result json was written to GCA_902767865.1_Rumen_uncultured_genome_RUG11299_genomic.fna/dqc_result.json
[2023-06-05 23:14:38,659] [INFO] DFAST_QC completed!
[2023-06-05 23:14:38,659] [INFO] Total running time: 0h0m42s