[2023-06-05 18:45:28,115] [INFO] DFAST_QC pipeline started.
[2023-06-05 18:45:28,117] [INFO] DFAST_QC version: 0.5.7
[2023-06-05 18:45:28,117] [INFO] DQC Reference Directory: /var/lib/cwl/stg8ca85a7a-73c0-4e2f-9a75-2c1d9bdd2896/dqc_reference
[2023-06-05 18:45:29,238] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-05 18:45:29,238] [INFO] Task started: Prodigal
[2023-06-05 18:45:29,238] [INFO] Running command: gunzip -c /var/lib/cwl/stg5648f457-e7e6-4f06-801a-ded9063368b6/GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna.gz | prodigal -d GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/cds.fna -a GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-05 18:45:33,409] [INFO] Task succeeded: Prodigal
[2023-06-05 18:45:33,410] [INFO] Task started: HMMsearch
[2023-06-05 18:45:33,410] [INFO] Running command: hmmsearch --tblout GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8ca85a7a-73c0-4e2f-9a75-2c1d9bdd2896/dqc_reference/reference_markers.hmm GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/protein.faa > /dev/null
[2023-06-05 18:45:33,780] [INFO] Task succeeded: HMMsearch
[2023-06-05 18:45:33,781] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg5648f457-e7e6-4f06-801a-ded9063368b6/GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna.gz]
[2023-06-05 18:45:33,811] [INFO] Query marker FASTA was written to GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/markers.fasta
[2023-06-05 18:45:33,811] [INFO] Task started: Blastn
[2023-06-05 18:45:33,811] [INFO] Running command: blastn -query GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ca85a7a-73c0-4e2f-9a75-2c1d9bdd2896/dqc_reference/reference_markers.fasta -out GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:45:34,251] [INFO] Task succeeded: Blastn
[2023-06-05 18:45:34,254] [INFO] Selected 3 target genomes.
[2023-06-05 18:45:34,254] [INFO] Target genome list was writen to GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/target_genomes.txt
[2023-06-05 18:45:34,255] [INFO] Task started: fastANI
[2023-06-05 18:45:34,255] [INFO] Running command: fastANI --query /var/lib/cwl/stg5648f457-e7e6-4f06-801a-ded9063368b6/GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna.gz --refList GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/target_genomes.txt --output GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/fastani_result.tsv --threads 1
[2023-06-05 18:45:35,359] [INFO] Task succeeded: fastANI
[2023-06-05 18:45:35,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8ca85a7a-73c0-4e2f-9a75-2c1d9bdd2896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-05 18:45:35,360] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8ca85a7a-73c0-4e2f-9a75-2c1d9bdd2896/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-05 18:45:35,364] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-05 18:45:35,364] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-05 18:45:35,364] [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	80.4294	284	721	95	below_threshold
Methanobrevibacter woesei	strain=DSM 11979	GCA_003111605.1	190976	190976	type	True	78.7326	148	721	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-05 18:45:35,366] [INFO] DFAST Taxonomy check result was written to GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/tc_result.tsv
[2023-06-05 18:45:35,367] [INFO] ===== Taxonomy check completed =====
[2023-06-05 18:45:35,367] [INFO] ===== Start completeness check using CheckM =====
[2023-06-05 18:45:35,367] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8ca85a7a-73c0-4e2f-9a75-2c1d9bdd2896/dqc_reference/checkm_data
[2023-06-05 18:45:35,368] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-05 18:45:35,398] [INFO] Task started: CheckM
[2023-06-05 18:45:35,398] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/checkm_input GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/checkm_result
[2023-06-05 18:45:56,283] [INFO] Task succeeded: CheckM
[2023-06-05 18:45:56,284] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 71.91%
Contamintation: 4.55%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-05 18:45:56,298] [INFO] ===== Completeness check finished =====
[2023-06-05 18:45:56,298] [INFO] ===== Start GTDB Search =====
[2023-06-05 18:45:56,299] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/markers.fasta)
[2023-06-05 18:45:56,299] [INFO] Task started: Blastn
[2023-06-05 18:45:56,299] [INFO] Running command: blastn -query GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/markers.fasta -db /var/lib/cwl/stg8ca85a7a-73c0-4e2f-9a75-2c1d9bdd2896/dqc_reference/reference_markers_gtdb.fasta -out GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-05 18:45:56,722] [INFO] Task succeeded: Blastn
[2023-06-05 18:45:56,724] [INFO] Selected 7 target genomes.
[2023-06-05 18:45:56,724] [INFO] Target genome list was writen to GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/target_genomes_gtdb.txt
[2023-06-05 18:45:56,794] [INFO] Task started: fastANI
[2023-06-05 18:45:56,794] [INFO] Running command: fastANI --query /var/lib/cwl/stg5648f457-e7e6-4f06-801a-ded9063368b6/GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna.gz --refList GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/target_genomes_gtdb.txt --output GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-05 18:46:00,341] [INFO] Task succeeded: fastANI
[2023-06-05 18:46:00,347] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-05 18:46:00,347] [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	97.988	496	721	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	90.6494	382	721	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	84.6059	391	721	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	84.424	390	721	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	81.5811	292	721	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	81.4507	325	721	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_017409525.1	s__Methanobrevibacter_A sp017409525	81.0379	299	721	d__Archaea;p__Methanobacteriota;c__Methanobacteria;o__Methanobacteriales;f__Methanobacteriaceae;g__Methanobrevibacter_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-05 18:46:00,349] [INFO] GTDB search result was written to GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/result_gtdb.tsv
[2023-06-05 18:46:00,349] [INFO] ===== GTDB Search completed =====
[2023-06-05 18:46:00,352] [INFO] DFAST_QC result json was written to GCA_902798355.1_Rumen_uncultured_genome_RUG14362_genomic.fna/dqc_result.json
[2023-06-05 18:46:00,352] [INFO] DFAST_QC completed!
[2023-06-05 18:46:00,352] [INFO] Total running time: 0h0m32s