[2023-06-08 03:42:22,932] [INFO] DFAST_QC pipeline started.
[2023-06-08 03:42:22,935] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 03:42:22,935] [INFO] DQC Reference Directory: /var/lib/cwl/stgf1aaf2cc-ef06-4f62-a024-3c0e8ce4e101/dqc_reference
[2023-06-08 03:42:24,256] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 03:42:24,257] [INFO] Task started: Prodigal
[2023-06-08 03:42:24,258] [INFO] Running command: gunzip -c /var/lib/cwl/stg813e1c66-6f68-4107-acdb-99b2cfee56db/GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna.gz | prodigal -d GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/cds.fna -a GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 03:42:26,415] [INFO] Task succeeded: Prodigal
[2023-06-08 03:42:26,416] [INFO] Task started: HMMsearch
[2023-06-08 03:42:26,416] [INFO] Running command: hmmsearch --tblout GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf1aaf2cc-ef06-4f62-a024-3c0e8ce4e101/dqc_reference/reference_markers.hmm GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/protein.faa > /dev/null
[2023-06-08 03:42:26,614] [INFO] Task succeeded: HMMsearch
[2023-06-08 03:42:26,615] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg813e1c66-6f68-4107-acdb-99b2cfee56db/GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna.gz]
[2023-06-08 03:42:26,637] [INFO] Query marker FASTA was written to GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/markers.fasta
[2023-06-08 03:42:26,637] [INFO] Task started: Blastn
[2023-06-08 03:42:26,637] [INFO] Running command: blastn -query GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1aaf2cc-ef06-4f62-a024-3c0e8ce4e101/dqc_reference/reference_markers.fasta -out GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:27,207] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:27,211] [INFO] Selected 19 target genomes.
[2023-06-08 03:42:27,211] [INFO] Target genome list was writen to GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/target_genomes.txt
[2023-06-08 03:42:27,213] [INFO] Task started: fastANI
[2023-06-08 03:42:27,213] [INFO] Running command: fastANI --query /var/lib/cwl/stg813e1c66-6f68-4107-acdb-99b2cfee56db/GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna.gz --refList GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/target_genomes.txt --output GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 03:42:35,180] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:35,180] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf1aaf2cc-ef06-4f62-a024-3c0e8ce4e101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 03:42:35,181] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf1aaf2cc-ef06-4f62-a024-3c0e8ce4e101/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 03:42:35,182] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 03:42:35,183] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 03:42:35,183] [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
--------------------------------------------------------------------------------
[2023-06-08 03:42:35,185] [INFO] DFAST Taxonomy check result was written to GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/tc_result.tsv
[2023-06-08 03:42:35,186] [INFO] ===== Taxonomy check completed =====
[2023-06-08 03:42:35,186] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 03:42:35,186] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf1aaf2cc-ef06-4f62-a024-3c0e8ce4e101/dqc_reference/checkm_data
[2023-06-08 03:42:35,189] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 03:42:35,206] [INFO] Task started: CheckM
[2023-06-08 03:42:35,206] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/checkm_input GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/checkm_result
[2023-06-08 03:42:50,099] [INFO] Task succeeded: CheckM
[2023-06-08 03:42:50,100] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 03:42:50,116] [INFO] ===== Completeness check finished =====
[2023-06-08 03:42:50,116] [INFO] ===== Start GTDB Search =====
[2023-06-08 03:42:50,117] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/markers.fasta)
[2023-06-08 03:42:50,117] [INFO] Task started: Blastn
[2023-06-08 03:42:50,117] [INFO] Running command: blastn -query GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/markers.fasta -db /var/lib/cwl/stgf1aaf2cc-ef06-4f62-a024-3c0e8ce4e101/dqc_reference/reference_markers_gtdb.fasta -out GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 03:42:50,946] [INFO] Task succeeded: Blastn
[2023-06-08 03:42:50,949] [INFO] Selected 18 target genomes.
[2023-06-08 03:42:50,950] [INFO] Target genome list was writen to GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 03:42:50,951] [INFO] Task started: fastANI
[2023-06-08 03:42:50,951] [INFO] Running command: fastANI --query /var/lib/cwl/stg813e1c66-6f68-4107-acdb-99b2cfee56db/GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna.gz --refList GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/target_genomes_gtdb.txt --output GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 03:42:55,141] [INFO] Task succeeded: fastANI
[2023-06-08 03:42:55,153] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 03:42:55,154] [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_902800945.1	s__Coprovivens sp902800945	100.0	442	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018711445.1	s__Coprovivens excrementavium	77.589	60	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017525015.1	s__Coprovivens sp017525015	77.5729	50	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900552975.1	s__Coprovivens sp900552975	77.4633	55	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	98.99	97.98	0.86	0.82	3	-
GCA_002362595.1	s__Coprovivens sp002362595	77.1349	55	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	99.46	99.46	0.78	0.78	2	-
GCA_910584655.1	s__Coprovivens sp910584655	77.0612	91	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016296185.1	s__Coprovivens sp016296185	76.7016	79	445	d__Bacteria;p__Firmicutes;c__Bacilli;o__RF39;f__UBA660;g__Coprovivens	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 03:42:55,155] [INFO] GTDB search result was written to GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/result_gtdb.tsv
[2023-06-08 03:42:55,156] [INFO] ===== GTDB Search completed =====
[2023-06-08 03:42:55,159] [INFO] DFAST_QC result json was written to GCA_902800945.1_Rumen_uncultured_genome_RUG14620_genomic.fna/dqc_result.json
[2023-06-08 03:42:55,159] [INFO] DFAST_QC completed!
[2023-06-08 03:42:55,159] [INFO] Total running time: 0h0m32s