[2023-06-08 19:01:14,870] [INFO] DFAST_QC pipeline started.
[2023-06-08 19:01:14,873] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 19:01:14,873] [INFO] DQC Reference Directory: /var/lib/cwl/stg04cd747d-7272-450a-ad4b-8e7639005da6/dqc_reference
[2023-06-08 19:01:16,142] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 19:01:16,143] [INFO] Task started: Prodigal
[2023-06-08 19:01:16,144] [INFO] Running command: gunzip -c /var/lib/cwl/stgec18580f-3709-4fbd-a8fb-176e0836b3fd/GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna.gz | prodigal -d GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/cds.fna -a GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 19:01:22,094] [INFO] Task succeeded: Prodigal
[2023-06-08 19:01:22,094] [INFO] Task started: HMMsearch
[2023-06-08 19:01:22,094] [INFO] Running command: hmmsearch --tblout GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg04cd747d-7272-450a-ad4b-8e7639005da6/dqc_reference/reference_markers.hmm GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/protein.faa > /dev/null
[2023-06-08 19:01:22,338] [INFO] Task succeeded: HMMsearch
[2023-06-08 19:01:22,340] [INFO] Found 6/6 markers.
[2023-06-08 19:01:22,367] [INFO] Query marker FASTA was written to GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/markers.fasta
[2023-06-08 19:01:22,367] [INFO] Task started: Blastn
[2023-06-08 19:01:22,367] [INFO] Running command: blastn -query GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cd747d-7272-450a-ad4b-8e7639005da6/dqc_reference/reference_markers.fasta -out GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:22,998] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:23,002] [INFO] Selected 16 target genomes.
[2023-06-08 19:01:23,003] [INFO] Target genome list was writen to GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/target_genomes.txt
[2023-06-08 19:01:23,008] [INFO] Task started: fastANI
[2023-06-08 19:01:23,008] [INFO] Running command: fastANI --query /var/lib/cwl/stgec18580f-3709-4fbd-a8fb-176e0836b3fd/GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna.gz --refList GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/target_genomes.txt --output GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 19:01:32,391] [INFO] Task succeeded: fastANI
[2023-06-08 19:01:32,392] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg04cd747d-7272-450a-ad4b-8e7639005da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 19:01:32,392] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg04cd747d-7272-450a-ad4b-8e7639005da6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 19:01:32,394] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 19:01:32,394] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-08 19:01:32,395] [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 19:01:32,397] [INFO] DFAST Taxonomy check result was written to GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/tc_result.tsv
[2023-06-08 19:01:32,398] [INFO] ===== Taxonomy check completed =====
[2023-06-08 19:01:32,398] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 19:01:32,398] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg04cd747d-7272-450a-ad4b-8e7639005da6/dqc_reference/checkm_data
[2023-06-08 19:01:32,402] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 19:01:32,429] [INFO] Task started: CheckM
[2023-06-08 19:01:32,429] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/checkm_input GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/checkm_result
[2023-06-08 19:01:57,161] [INFO] Task succeeded: CheckM
[2023-06-08 19:01:57,163] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 79.17%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 19:01:57,184] [INFO] ===== Completeness check finished =====
[2023-06-08 19:01:57,184] [INFO] ===== Start GTDB Search =====
[2023-06-08 19:01:57,184] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/markers.fasta)
[2023-06-08 19:01:57,185] [INFO] Task started: Blastn
[2023-06-08 19:01:57,185] [INFO] Running command: blastn -query GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/markers.fasta -db /var/lib/cwl/stg04cd747d-7272-450a-ad4b-8e7639005da6/dqc_reference/reference_markers_gtdb.fasta -out GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 19:01:58,191] [INFO] Task succeeded: Blastn
[2023-06-08 19:01:58,196] [INFO] Selected 11 target genomes.
[2023-06-08 19:01:58,196] [INFO] Target genome list was writen to GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 19:01:58,199] [INFO] Task started: fastANI
[2023-06-08 19:01:58,199] [INFO] Running command: fastANI --query /var/lib/cwl/stgec18580f-3709-4fbd-a8fb-176e0836b3fd/GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna.gz --refList GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/target_genomes_gtdb.txt --output GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 19:02:03,142] [INFO] Task succeeded: fastANI
[2023-06-08 19:02:03,150] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 19:02:03,150] [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_902786355.1	s__RUG099 sp902786355	100.0	804	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900315485.1	s__RUG099 sp900315485	83.1997	362	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	97.58	95.36	0.86	0.78	12	-
GCA_902765035.1	s__RUG099 sp902765035	82.5808	226	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900317675.1	s__RUG099 sp900317675	81.3266	374	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	99.00	98.41	0.81	0.74	5	-
GCA_017512145.1	s__RUG099 sp017512145	81.013	252	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	98.30	98.30	0.88	0.88	2	-
GCA_902786855.1	s__RUG099 sp902786855	80.4652	344	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017431175.1	s__RUG099 sp017431175	79.8808	282	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017434025.1	s__RUG099 sp017434025	79.3791	228	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902760855.1	s__RUG099 sp902760855	77.6841	89	804	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Peptostreptococcales;f__Anaerovoracaceae;g__RUG099	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 19:02:03,156] [INFO] GTDB search result was written to GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/result_gtdb.tsv
[2023-06-08 19:02:03,156] [INFO] ===== GTDB Search completed =====
[2023-06-08 19:02:03,159] [INFO] DFAST_QC result json was written to GCA_902786355.1_Rumen_uncultured_genome_RUG13158_genomic.fna/dqc_result.json
[2023-06-08 19:02:03,159] [INFO] DFAST_QC completed!
[2023-06-08 19:02:03,159] [INFO] Total running time: 0h0m48s