[2023-06-05 00:38:09,766] [INFO] DFAST_QC pipeline started.
[2023-06-05 00:38:09,769] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 00:38:09,769] [INFO] DQC Reference Directory: /var/lib/cwl/stg16c705bc-7ca8-42c2-9b8e-0f579754ab2a/dqc_reference
[2023-06-05 00:38:11,457] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 00:38:11,458] [INFO] Task started: Prodigal
[2023-06-05 00:38:11,459] [INFO] Running command: gunzip -c /var/lib/cwl/stg5a4a2d61-3ef8-4382-abe3-f7a5ec73c9fa/GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna.gz | prodigal -d GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/cds.fna -a GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 00:38:13,526] [INFO] Task succeeded: Prodigal
[2023-06-05 00:38:13,527] [INFO] Task started: HMMsearch
[2023-06-05 00:38:13,527] [INFO] Running command: hmmsearch --tblout GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg16c705bc-7ca8-42c2-9b8e-0f579754ab2a/dqc_reference/reference_markers.hmm GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/protein.faa > /dev/null
[2023-06-05 00:38:13,784] [INFO] Task succeeded: HMMsearch
[2023-06-05 00:38:13,785] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg5a4a2d61-3ef8-4382-abe3-f7a5ec73c9fa/GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna.gz]
[2023-06-05 00:38:13,803] [INFO] Query marker FASTA was written to GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/markers.fasta
[2023-06-05 00:38:13,803] [INFO] Task started: Blastn
[2023-06-05 00:38:13,804] [INFO] Running command: blastn -query GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c705bc-7ca8-42c2-9b8e-0f579754ab2a/dqc_reference/reference_markers.fasta -out GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:14,392] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:14,396] [INFO] Selected 21 target genomes.
[2023-06-05 00:38:14,396] [INFO] Target genome list was writen to GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/target_genomes.txt
[2023-06-05 00:38:14,429] [INFO] Task started: fastANI
[2023-06-05 00:38:14,429] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4a2d61-3ef8-4382-abe3-f7a5ec73c9fa/GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna.gz --refList GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/target_genomes.txt --output GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 00:38:23,013] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:23,014] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg16c705bc-7ca8-42c2-9b8e-0f579754ab2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 00:38:23,014] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg16c705bc-7ca8-42c2-9b8e-0f579754ab2a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 00:38:23,016] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 00:38:23,016] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 00:38:23,016] [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 00:38:23,018] [INFO] DFAST Taxonomy check result was written to GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/tc_result.tsv
[2023-06-05 00:38:23,018] [INFO] ===== Taxonomy check completed =====
[2023-06-05 00:38:23,019] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 00:38:23,019] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg16c705bc-7ca8-42c2-9b8e-0f579754ab2a/dqc_reference/checkm_data
[2023-06-05 00:38:23,021] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 00:38:23,035] [INFO] Task started: CheckM
[2023-06-05 00:38:23,036] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/checkm_input GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/checkm_result
[2023-06-05 00:38:37,941] [INFO] Task succeeded: CheckM
[2023-06-05 00:38:37,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 62.50%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 00:38:37,962] [INFO] ===== Completeness check finished =====
[2023-06-05 00:38:37,963] [INFO] ===== Start GTDB Search =====
[2023-06-05 00:38:37,963] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/markers.fasta)
[2023-06-05 00:38:37,964] [INFO] Task started: Blastn
[2023-06-05 00:38:37,964] [INFO] Running command: blastn -query GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/markers.fasta -db /var/lib/cwl/stg16c705bc-7ca8-42c2-9b8e-0f579754ab2a/dqc_reference/reference_markers_gtdb.fasta -out GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 00:38:38,733] [INFO] Task succeeded: Blastn
[2023-06-05 00:38:38,737] [INFO] Selected 13 target genomes.
[2023-06-05 00:38:38,737] [INFO] Target genome list was writen to GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 00:38:38,746] [INFO] Task started: fastANI
[2023-06-05 00:38:38,747] [INFO] Running command: fastANI --query /var/lib/cwl/stg5a4a2d61-3ef8-4382-abe3-f7a5ec73c9fa/GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna.gz --refList GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/target_genomes_gtdb.txt --output GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 00:38:41,994] [INFO] Task succeeded: fastANI
[2023-06-05 00:38:42,012] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 00:38:42,012] [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_902797795.1	s__UBA2450 sp902797795	100.0	350	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900314865.1	s__UBA2450 sp900314865	81.6355	216	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	100.00	100.00	1.00	1.00	2	-
GCA_902800645.1	s__UBA2450 sp902800645	80.0047	126	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002353275.1	s__UBA2450 sp002353275	79.4992	137	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800905.1	s__UBA2450 sp902800905	79.4897	144	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902800025.1	s__UBA2450 sp902800025	79.3829	145	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	97.35	97.35	0.90	0.90	2	-
GCA_017635565.1	s__UBA2450 sp017635565	79.0424	84	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002373085.1	s__UBA2450 sp002373085	79.014	106	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	95.60	95.60	0.78	0.78	2	-
GCA_902800355.1	s__UBA2450 sp902800355	78.9017	117	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002342545.1	s__UBA2450 sp002342545	78.4056	125	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__UBA2450	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902785645.1	s__RUG13091 sp902785645	77.1344	54	353	d__Bacteria;p__Firmicutes;c__Bacilli;o__RFN20;f__CAG-826;g__RUG13091	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 00:38:42,014] [INFO] GTDB search result was written to GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/result_gtdb.tsv
[2023-06-05 00:38:42,015] [INFO] ===== GTDB Search completed =====
[2023-06-05 00:38:42,019] [INFO] DFAST_QC result json was written to GCA_902797795.1_Rumen_uncultured_genome_RUG14307_genomic.fna/dqc_result.json
[2023-06-05 00:38:42,020] [INFO] DFAST_QC completed!
[2023-06-05 00:38:42,020] [INFO] Total running time: 0h0m32s