[2023-06-05 05:55:40,730] [INFO] DFAST_QC pipeline started.
[2023-06-05 05:55:40,734] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 05:55:40,735] [INFO] DQC Reference Directory: /var/lib/cwl/stge0ece432-8195-417d-924e-6dc4a282c2d3/dqc_reference
[2023-06-05 05:55:43,091] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 05:55:43,092] [INFO] Task started: Prodigal
[2023-06-05 05:55:43,092] [INFO] Running command: gunzip -c /var/lib/cwl/stged97c7d2-5f75-47eb-bdb0-a6bc9557eb4d/GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna.gz | prodigal -d GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/cds.fna -a GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 05:55:54,761] [INFO] Task succeeded: Prodigal
[2023-06-05 05:55:54,762] [INFO] Task started: HMMsearch
[2023-06-05 05:55:54,762] [INFO] Running command: hmmsearch --tblout GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge0ece432-8195-417d-924e-6dc4a282c2d3/dqc_reference/reference_markers.hmm GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/protein.faa > /dev/null
[2023-06-05 05:55:55,046] [INFO] Task succeeded: HMMsearch
[2023-06-05 05:55:55,048] [INFO] Found 6/6 markers.
[2023-06-05 05:55:55,094] [INFO] Query marker FASTA was written to GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/markers.fasta
[2023-06-05 05:55:55,094] [INFO] Task started: Blastn
[2023-06-05 05:55:55,095] [INFO] Running command: blastn -query GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/markers.fasta -db /var/lib/cwl/stge0ece432-8195-417d-924e-6dc4a282c2d3/dqc_reference/reference_markers.fasta -out GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:55:55,705] [INFO] Task succeeded: Blastn
[2023-06-05 05:55:55,711] [INFO] Selected 35 target genomes.
[2023-06-05 05:55:55,711] [INFO] Target genome list was writen to GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/target_genomes.txt
[2023-06-05 05:55:55,717] [INFO] Task started: fastANI
[2023-06-05 05:55:55,717] [INFO] Running command: fastANI --query /var/lib/cwl/stged97c7d2-5f75-47eb-bdb0-a6bc9557eb4d/GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna.gz --refList GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/target_genomes.txt --output GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 05:56:19,504] [INFO] Task succeeded: fastANI
[2023-06-05 05:56:19,505] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge0ece432-8195-417d-924e-6dc4a282c2d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 05:56:19,505] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge0ece432-8195-417d-924e-6dc4a282c2d3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 05:56:19,508] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 05:56:19,508] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-05 05:56:19,508] [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 05:56:19,510] [INFO] DFAST Taxonomy check result was written to GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/tc_result.tsv
[2023-06-05 05:56:19,511] [INFO] ===== Taxonomy check completed =====
[2023-06-05 05:56:19,512] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 05:56:19,512] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge0ece432-8195-417d-924e-6dc4a282c2d3/dqc_reference/checkm_data
[2023-06-05 05:56:19,516] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 05:56:19,565] [INFO] Task started: CheckM
[2023-06-05 05:56:19,566] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/checkm_input GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/checkm_result
[2023-06-05 05:56:56,767] [INFO] Task succeeded: CheckM
[2023-06-05 05:56:56,769] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-05 05:56:56,792] [INFO] ===== Completeness check finished =====
[2023-06-05 05:56:56,792] [INFO] ===== Start GTDB Search =====
[2023-06-05 05:56:56,793] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/markers.fasta)
[2023-06-05 05:56:56,793] [INFO] Task started: Blastn
[2023-06-05 05:56:56,793] [INFO] Running command: blastn -query GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/markers.fasta -db /var/lib/cwl/stge0ece432-8195-417d-924e-6dc4a282c2d3/dqc_reference/reference_markers_gtdb.fasta -out GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 05:56:57,704] [INFO] Task succeeded: Blastn
[2023-06-05 05:56:57,709] [INFO] Selected 8 target genomes.
[2023-06-05 05:56:57,709] [INFO] Target genome list was writen to GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 05:56:57,715] [INFO] Task started: fastANI
[2023-06-05 05:56:57,716] [INFO] Running command: fastANI --query /var/lib/cwl/stged97c7d2-5f75-47eb-bdb0-a6bc9557eb4d/GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna.gz --refList GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/target_genomes_gtdb.txt --output GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 05:57:04,707] [INFO] Task succeeded: fastANI
[2023-06-05 05:57:04,715] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 05:57:04,715] [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_902776645.1	s__UBA1407 sp902776645	97.3092	1069	1209	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__UBA1407	95.0	97.32	96.58	0.88	0.85	5	conclusive
GCA_017554445.1	s__UBA1407 sp017554445	87.0566	973	1209	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__UBA1407	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017548425.1	s__UBA1407 sp017548425	86.6672	962	1209	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__UBA1407	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017964325.1	s__UBA1407 sp017964325	84.9531	817	1209	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__UBA1407	95.0	96.33	96.33	0.83	0.83	2	-
GCA_900769285.1	s__CAAGGB01 sp900769285	77.3719	160	1209	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__CAAGGB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017458805.1	s__RGIG3456 sp017458805	76.7455	83	1209	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__RGIG3456	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902783355.1	s__CACZQQ01 sp902783355	76.1693	63	1209	d__Bacteria;p__Verrucomicrobiota;c__Lentisphaeria;o__UBA1407;f__UBA1407;g__CACZQQ01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 05:57:04,717] [INFO] GTDB search result was written to GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/result_gtdb.tsv
[2023-06-05 05:57:04,718] [INFO] ===== GTDB Search completed =====
[2023-06-05 05:57:04,721] [INFO] DFAST_QC result json was written to GCA_902780595.1_Rumen_uncultured_genome_RUG12584_genomic.fna/dqc_result.json
[2023-06-05 05:57:04,721] [INFO] DFAST_QC completed!
[2023-06-05 05:57:04,721] [INFO] Total running time: 0h1m24s