[2023-06-08 14:53:58,635] [INFO] DFAST_QC pipeline started.
[2023-06-08 14:53:58,643] [INFO] DFAST_QC version: 0.5.7
[2023-06-08 14:53:58,643] [INFO] DQC Reference Directory: /var/lib/cwl/stg36ac0be3-1e98-4213-b4c6-1ed28303df78/dqc_reference
[2023-06-08 14:54:00,745] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-08 14:54:00,746] [INFO] Task started: Prodigal
[2023-06-08 14:54:00,746] [INFO] Running command: gunzip -c /var/lib/cwl/stg2df4cdc0-0374-473b-8382-c858a24b5851/GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna.gz | prodigal -d GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/cds.fna -a GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-08 14:54:04,098] [INFO] Task succeeded: Prodigal
[2023-06-08 14:54:04,099] [INFO] Task started: HMMsearch
[2023-06-08 14:54:04,099] [INFO] Running command: hmmsearch --tblout GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg36ac0be3-1e98-4213-b4c6-1ed28303df78/dqc_reference/reference_markers.hmm GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/protein.faa > /dev/null
[2023-06-08 14:54:04,298] [INFO] Task succeeded: HMMsearch
[2023-06-08 14:54:04,299] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg2df4cdc0-0374-473b-8382-c858a24b5851/GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna.gz]
[2023-06-08 14:54:04,325] [INFO] Query marker FASTA was written to GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/markers.fasta
[2023-06-08 14:54:04,325] [INFO] Task started: Blastn
[2023-06-08 14:54:04,325] [INFO] Running command: blastn -query GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/markers.fasta -db /var/lib/cwl/stg36ac0be3-1e98-4213-b4c6-1ed28303df78/dqc_reference/reference_markers.fasta -out GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:54:05,146] [INFO] Task succeeded: Blastn
[2023-06-08 14:54:05,151] [INFO] Selected 5 target genomes.
[2023-06-08 14:54:05,151] [INFO] Target genome list was writen to GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/target_genomes.txt
[2023-06-08 14:54:05,152] [INFO] Task started: fastANI
[2023-06-08 14:54:05,153] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df4cdc0-0374-473b-8382-c858a24b5851/GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna.gz --refList GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/target_genomes.txt --output GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/fastani_result.tsv --threads 1
[2023-06-08 14:54:07,157] [INFO] Task succeeded: fastANI
[2023-06-08 14:54:07,158] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg36ac0be3-1e98-4213-b4c6-1ed28303df78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-08 14:54:07,158] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg36ac0be3-1e98-4213-b4c6-1ed28303df78/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-08 14:54:07,170] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-08 14:54:07,170] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-08 14:54:07,171] [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 millerae	strain=DSM 16643	GCA_900103415.1	230361	230361	type	True	80.363	276	564	95	below_threshold
Methanobrevibacter thaueri	strain=DSM 11995	GCA_003111625.1	190975	190975	type	True	79.9411	197	564	95	below_threshold
Methanobrevibacter woesei	strain=DSM 11979	GCA_003111605.1	190976	190976	type	True	79.2551	145	564	95	below_threshold
Methanobrevibacter smithii	strain=ATCC 35061; PS; DSMZ 861	GCA_000016525.1	2173	2173	type	True	79.0474	202	564	95	below_threshold
Methanobrevibacter olleyae	strain=DSM 16632	GCA_900114585.1	294671	294671	type	True	77.1175	101	564	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-08 14:54:07,175] [INFO] DFAST Taxonomy check result was written to GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/tc_result.tsv
[2023-06-08 14:54:07,176] [INFO] ===== Taxonomy check completed =====
[2023-06-08 14:54:07,176] [INFO] ===== Start completeness check using CheckM =====
[2023-06-08 14:54:07,177] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg36ac0be3-1e98-4213-b4c6-1ed28303df78/dqc_reference/checkm_data
[2023-06-08 14:54:07,179] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-08 14:54:07,212] [INFO] Task started: CheckM
[2023-06-08 14:54:07,212] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/checkm_input GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/checkm_result
[2023-06-08 14:54:25,204] [INFO] Task succeeded: CheckM
[2023-06-08 14:54:25,206] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 70.45%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-08 14:54:25,228] [INFO] ===== Completeness check finished =====
[2023-06-08 14:54:25,228] [INFO] ===== Start GTDB Search =====
[2023-06-08 14:54:25,228] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/markers.fasta)
[2023-06-08 14:54:25,229] [INFO] Task started: Blastn
[2023-06-08 14:54:25,229] [INFO] Running command: blastn -query GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/markers.fasta -db /var/lib/cwl/stg36ac0be3-1e98-4213-b4c6-1ed28303df78/dqc_reference/reference_markers_gtdb.fasta -out GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-08 14:54:25,869] [INFO] Task succeeded: Blastn
[2023-06-08 14:54:25,874] [INFO] Selected 12 target genomes.
[2023-06-08 14:54:25,874] [INFO] Target genome list was writen to GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/target_genomes_gtdb.txt
[2023-06-08 14:54:25,877] [INFO] Task started: fastANI
[2023-06-08 14:54:25,878] [INFO] Running command: fastANI --query /var/lib/cwl/stg2df4cdc0-0374-473b-8382-c858a24b5851/GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna.gz --refList GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/target_genomes_gtdb.txt --output GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-08 14:54:31,308] [INFO] Task succeeded: fastANI
[2023-06-08 14:54:31,324] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-08 14:54:31,324] [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
GCF_001477655.1	s__Methanobrevibacter_A millerae_A	97.9957	497	564	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_015063005.1	s__Methanobrevibacter_A millerae_B	84.3169	364	564	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	97.89	97.89	0.85	0.85	2	-
GCA_017434555.1	s__Methanobrevibacter_A sp017434555	83.2915	364	564	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.09	97.80	0.83	0.83	3	-
GCA_902771225.1	s__Methanobrevibacter_A sp900319535	83.1026	335	564	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_900317865.1	s__Methanobrevibacter_A sp900317865	83.0932	323	564	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	98.42	95.98	0.84	0.76	8	-
GCA_017553445.1	s__Methanobrevibacter_A sp017553445	82.9545	287	564	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_902777885.1	s__Methanobrevibacter_A sp902777885	82.8533	212	564	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_902785855.1	s__Methanobrevibacter_A sp902785855	80.0484	220	564	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	97.27	97.27	0.75	0.75	2	-
GCA_902783085.1	s__Methanobrevibacter_A sp902783085	79.9298	201	564	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_017407115.1	s__Methanobrevibacter_A sp017407115	79.8588	191	564	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_017539065.1	s__Methanobrevibacter_A sp017539065	79.8078	192	564	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_017459665.1	s__Methanobrevibacter_A sp017459665	79.0888	189	564	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-08 14:54:31,326] [INFO] GTDB search result was written to GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/result_gtdb.tsv
[2023-06-08 14:54:31,327] [INFO] ===== GTDB Search completed =====
[2023-06-08 14:54:31,331] [INFO] DFAST_QC result json was written to GCA_902793735.1_Rumen_uncultured_genome_RUG13892_genomic.fna/dqc_result.json
[2023-06-08 14:54:31,331] [INFO] DFAST_QC completed!
[2023-06-08 14:54:31,331] [INFO] Total running time: 0h0m33s