[2023-06-07 20:40:03,137] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:40:03,144] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:40:03,144] [INFO] DQC Reference Directory: /var/lib/cwl/stg23fc98f8-86ec-41c8-a371-a0fad07f5ece/dqc_reference
[2023-06-07 20:40:04,630] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:40:04,631] [INFO] Task started: Prodigal
[2023-06-07 20:40:04,631] [INFO] Running command: gunzip -c /var/lib/cwl/stgd50659b6-4572-4158-b152-2e3fbaae458c/GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna.gz | prodigal -d GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/cds.fna -a GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:40:07,829] [INFO] Task succeeded: Prodigal
[2023-06-07 20:40:07,829] [INFO] Task started: HMMsearch
[2023-06-07 20:40:07,830] [INFO] Running command: hmmsearch --tblout GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23fc98f8-86ec-41c8-a371-a0fad07f5ece/dqc_reference/reference_markers.hmm GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:40:08,038] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:40:08,039] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd50659b6-4572-4158-b152-2e3fbaae458c/GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna.gz]
[2023-06-07 20:40:08,061] [INFO] Query marker FASTA was written to GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/markers.fasta
[2023-06-07 20:40:08,062] [INFO] Task started: Blastn
[2023-06-07 20:40:08,062] [INFO] Running command: blastn -query GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/markers.fasta -db /var/lib/cwl/stg23fc98f8-86ec-41c8-a371-a0fad07f5ece/dqc_reference/reference_markers.fasta -out GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:08,687] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:08,692] [INFO] Selected 3 target genomes.
[2023-06-07 20:40:08,692] [INFO] Target genome list was writen to GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/target_genomes.txt
[2023-06-07 20:40:08,695] [INFO] Task started: fastANI
[2023-06-07 20:40:08,696] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50659b6-4572-4158-b152-2e3fbaae458c/GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna.gz --refList GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/target_genomes.txt --output GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:40:09,882] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:09,883] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23fc98f8-86ec-41c8-a371-a0fad07f5ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:40:09,884] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23fc98f8-86ec-41c8-a371-a0fad07f5ece/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:40:09,895] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:40:09,896] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:40:09,896] [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 gottschalkii	strain=DSM 11977	GCA_003814835.1	190974	190974	type	True	80.8433	226	447	95	below_threshold
Methanobrevibacter woesei	strain=DSM 11979	GCA_003111605.1	190976	190976	type	True	79.3544	133	447	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:40:09,898] [INFO] DFAST Taxonomy check result was written to GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/tc_result.tsv
[2023-06-07 20:40:09,898] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:40:09,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:40:09,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23fc98f8-86ec-41c8-a371-a0fad07f5ece/dqc_reference/checkm_data
[2023-06-07 20:40:09,900] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:40:09,926] [INFO] Task started: CheckM
[2023-06-07 20:40:09,926] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/checkm_input GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/checkm_result
[2023-06-07 20:40:27,979] [INFO] Task succeeded: CheckM
[2023-06-07 20:40:27,980] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 85.35%
Contamintation: 0.38%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:40:28,006] [INFO] ===== Completeness check finished =====
[2023-06-07 20:40:28,007] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:40:28,007] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/markers.fasta)
[2023-06-07 20:40:28,008] [INFO] Task started: Blastn
[2023-06-07 20:40:28,008] [INFO] Running command: blastn -query GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/markers.fasta -db /var/lib/cwl/stg23fc98f8-86ec-41c8-a371-a0fad07f5ece/dqc_reference/reference_markers_gtdb.fasta -out GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:40:28,679] [INFO] Task succeeded: Blastn
[2023-06-07 20:40:28,685] [INFO] Selected 12 target genomes.
[2023-06-07 20:40:28,686] [INFO] Target genome list was writen to GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:40:28,690] [INFO] Task started: fastANI
[2023-06-07 20:40:28,691] [INFO] Running command: fastANI --query /var/lib/cwl/stgd50659b6-4572-4158-b152-2e3fbaae458c/GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna.gz --refList GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/target_genomes_gtdb.txt --output GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:40:33,006] [INFO] Task succeeded: fastANI
[2023-06-07 20:40:33,014] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-07 20:40:33,015] [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_900314695.1	s__Methanobrevibacter_A sp900314695	99.08	380	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.43	97.20	0.85	0.69	27	conclusive
GCA_900320955.1	s__Methanobrevibacter_A sp900320955	91.4304	301	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	100.00	100.00	0.99	0.99	2	-
GCA_900319985.1	s__Methanobrevibacter_A sp900319985	84.9081	297	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	99.40	99.05	0.87	0.68	4	-
GCA_902801725.1	s__Methanobrevibacter_A sp902801725	84.4113	297	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902789505.1	s__Methanobrevibacter_A sp902789505	81.9775	234	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	96.82	96.82	0.70	0.70	2	-
GCA_017431965.1	s__Methanobrevibacter_A sp017431965	81.9191	261	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902771225.1	s__Methanobrevibacter_A sp900319535	80.6751	208	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.34	97.61	0.81	0.64	15	-
GCA_900313645.1	s__Methanobrevibacter_A sp900313645	80.5192	169	447	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.96	97.91	0.87	0.75	3	-
--------------------------------------------------------------------------------
[2023-06-07 20:40:33,017] [INFO] GTDB search result was written to GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/result_gtdb.tsv
[2023-06-07 20:40:33,017] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:40:33,020] [INFO] DFAST_QC result json was written to GCA_902757435.1_Rumen_uncultured_genome_RUG10261_genomic.fna/dqc_result.json
[2023-06-07 20:40:33,020] [INFO] DFAST_QC completed!
[2023-06-07 20:40:33,020] [INFO] Total running time: 0h0m30s