[2023-06-05 08:38:47,598] [INFO] DFAST_QC pipeline started.
[2023-06-05 08:38:47,600] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 08:38:47,600] [INFO] DQC Reference Directory: /var/lib/cwl/stg85bedecc-0c0c-4c0c-8554-f6a0b7c40508/dqc_reference
[2023-06-05 08:38:49,717] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 08:38:49,718] [INFO] Task started: Prodigal
[2023-06-05 08:38:49,718] [INFO] Running command: gunzip -c /var/lib/cwl/stge4297019-8249-4719-b49a-a51091c8349d/GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna.gz | prodigal -d GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/cds.fna -a GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 08:38:55,391] [INFO] Task succeeded: Prodigal
[2023-06-05 08:38:55,392] [INFO] Task started: HMMsearch
[2023-06-05 08:38:55,392] [INFO] Running command: hmmsearch --tblout GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg85bedecc-0c0c-4c0c-8554-f6a0b7c40508/dqc_reference/reference_markers.hmm GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/protein.faa > /dev/null
[2023-06-05 08:38:55,600] [INFO] Task succeeded: HMMsearch
[2023-06-05 08:38:55,602] [WARNING] Found 2/6 markers. [/var/lib/cwl/stge4297019-8249-4719-b49a-a51091c8349d/GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna.gz]
[2023-06-05 08:38:55,634] [INFO] Query marker FASTA was written to GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/markers.fasta
[2023-06-05 08:38:55,635] [INFO] Task started: Blastn
[2023-06-05 08:38:55,635] [INFO] Running command: blastn -query GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/markers.fasta -db /var/lib/cwl/stg85bedecc-0c0c-4c0c-8554-f6a0b7c40508/dqc_reference/reference_markers.fasta -out GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:38:56,132] [INFO] Task succeeded: Blastn
[2023-06-05 08:38:56,136] [INFO] Selected 3 target genomes.
[2023-06-05 08:38:56,136] [INFO] Target genome list was writen to GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/target_genomes.txt
[2023-06-05 08:38:56,139] [INFO] Task started: fastANI
[2023-06-05 08:38:56,139] [INFO] Running command: fastANI --query /var/lib/cwl/stge4297019-8249-4719-b49a-a51091c8349d/GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna.gz --refList GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/target_genomes.txt --output GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 08:38:58,227] [INFO] Task succeeded: fastANI
[2023-06-05 08:38:58,227] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg85bedecc-0c0c-4c0c-8554-f6a0b7c40508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 08:38:58,228] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg85bedecc-0c0c-4c0c-8554-f6a0b7c40508/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 08:38:58,236] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 08:38:58,236] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 08:38:58,236] [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
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	81.3026	453	1010	95	below_threshold
Methanobrevibacter ruminantium	strain=M1	GCA_000024185.1	83816	83816	type	True	80.073	452	1010	95	below_threshold
Methanobrevibacter millerae	strain=DSM 16643	GCA_900103415.1	230361	230361	type	True	76.0928	99	1010	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 08:38:58,238] [INFO] DFAST Taxonomy check result was written to GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/tc_result.tsv
[2023-06-05 08:38:58,239] [INFO] ===== Taxonomy check completed =====
[2023-06-05 08:38:58,239] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 08:38:58,239] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg85bedecc-0c0c-4c0c-8554-f6a0b7c40508/dqc_reference/checkm_data
[2023-06-05 08:38:58,240] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 08:38:58,277] [INFO] Task started: CheckM
[2023-06-05 08:38:58,278] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/checkm_input GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/checkm_result
[2023-06-05 08:39:22,204] [INFO] Task succeeded: CheckM
[2023-06-05 08:39:22,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.84%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 08:39:22,227] [INFO] ===== Completeness check finished =====
[2023-06-05 08:39:22,227] [INFO] ===== Start GTDB Search =====
[2023-06-05 08:39:22,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/markers.fasta)
[2023-06-05 08:39:22,228] [INFO] Task started: Blastn
[2023-06-05 08:39:22,228] [INFO] Running command: blastn -query GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/markers.fasta -db /var/lib/cwl/stg85bedecc-0c0c-4c0c-8554-f6a0b7c40508/dqc_reference/reference_markers_gtdb.fasta -out GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 08:39:22,734] [INFO] Task succeeded: Blastn
[2023-06-05 08:39:22,738] [INFO] Selected 8 target genomes.
[2023-06-05 08:39:22,738] [INFO] Target genome list was writen to GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 08:39:22,744] [INFO] Task started: fastANI
[2023-06-05 08:39:22,744] [INFO] Running command: fastANI --query /var/lib/cwl/stge4297019-8249-4719-b49a-a51091c8349d/GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna.gz --refList GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/target_genomes_gtdb.txt --output GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 08:39:28,018] [INFO] Task succeeded: fastANI
[2023-06-05 08:39:28,026] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 08:39:28,026] [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_902769175.1	s__Methanobrevibacter sp902769175	100.0	1008	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016291275.1	s__Methanobrevibacter sp016291275	84.4958	305	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017432245.1	s__Methanobrevibacter sp017432245	84.0317	415	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004553595.1	s__Methanobrevibacter ruminantium_A	83.8245	490	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	99.31	99.31	0.95	0.95	2	-
GCA_015063035.1	s__Methanobrevibacter olleyae_A	83.5268	484	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017646885.1	s__Methanobrevibacter sp017646885	83.2426	201	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017652345.1	s__Methanobrevibacter sp017652345	82.4129	155	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900114585.1	s__Methanobrevibacter olleyae	81.3078	453	1010	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter	95.0	99.51	99.51	0.97	0.97	2	-
--------------------------------------------------------------------------------
[2023-06-05 08:39:28,029] [INFO] GTDB search result was written to GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/result_gtdb.tsv
[2023-06-05 08:39:28,029] [INFO] ===== GTDB Search completed =====
[2023-06-05 08:39:28,033] [INFO] DFAST_QC result json was written to GCA_902769175.1_Rumen_uncultured_genome_RUG11428_genomic.fna/dqc_result.json
[2023-06-05 08:39:28,033] [INFO] DFAST_QC completed!
[2023-06-05 08:39:28,033] [INFO] Total running time: 0h0m40s