[2023-06-04 18:45:54,158] [INFO] DFAST_QC pipeline started.
[2023-06-04 18:45:54,165] [INFO] DFAST_QC version: 0.5.7
[2023-06-04 18:45:54,165] [INFO] DQC Reference Directory: /var/lib/cwl/stg12c080d7-37c0-448f-9415-2325c78baf1b/dqc_reference
[2023-06-04 18:45:55,591] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-04 18:45:55,591] [INFO] Task started: Prodigal
[2023-06-04 18:45:55,592] [INFO] Running command: gunzip -c /var/lib/cwl/stgac99241f-facc-4daa-a168-0fd9c0d27131/GCA_934552765.1_ERR7746411_bin.108_genomic.fna.gz | prodigal -d GCA_934552765.1_ERR7746411_bin.108_genomic.fna/cds.fna -a GCA_934552765.1_ERR7746411_bin.108_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-04 18:46:00,763] [INFO] Task succeeded: Prodigal
[2023-06-04 18:46:00,764] [INFO] Task started: HMMsearch
[2023-06-04 18:46:00,764] [INFO] Running command: hmmsearch --tblout GCA_934552765.1_ERR7746411_bin.108_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg12c080d7-37c0-448f-9415-2325c78baf1b/dqc_reference/reference_markers.hmm GCA_934552765.1_ERR7746411_bin.108_genomic.fna/protein.faa > /dev/null
[2023-06-04 18:46:01,023] [INFO] Task succeeded: HMMsearch
[2023-06-04 18:46:01,025] [INFO] Found 6/6 markers.
[2023-06-04 18:46:01,047] [INFO] Query marker FASTA was written to GCA_934552765.1_ERR7746411_bin.108_genomic.fna/markers.fasta
[2023-06-04 18:46:01,047] [INFO] Task started: Blastn
[2023-06-04 18:46:01,048] [INFO] Running command: blastn -query GCA_934552765.1_ERR7746411_bin.108_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c080d7-37c0-448f-9415-2325c78baf1b/dqc_reference/reference_markers.fasta -out GCA_934552765.1_ERR7746411_bin.108_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:46:01,672] [INFO] Task succeeded: Blastn
[2023-06-04 18:46:01,677] [INFO] Selected 23 target genomes.
[2023-06-04 18:46:01,677] [INFO] Target genome list was writen to GCA_934552765.1_ERR7746411_bin.108_genomic.fna/target_genomes.txt
[2023-06-04 18:46:01,768] [INFO] Task started: fastANI
[2023-06-04 18:46:01,769] [INFO] Running command: fastANI --query /var/lib/cwl/stgac99241f-facc-4daa-a168-0fd9c0d27131/GCA_934552765.1_ERR7746411_bin.108_genomic.fna.gz --refList GCA_934552765.1_ERR7746411_bin.108_genomic.fna/target_genomes.txt --output GCA_934552765.1_ERR7746411_bin.108_genomic.fna/fastani_result.tsv --threads 1
[2023-06-04 18:46:14,349] [INFO] Task succeeded: fastANI
[2023-06-04 18:46:14,350] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg12c080d7-37c0-448f-9415-2325c78baf1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-04 18:46:14,350] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg12c080d7-37c0-448f-9415-2325c78baf1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-04 18:46:14,354] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-04 18:46:14,354] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-04 18:46:14,354] [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
Eubacterium coprostanoligenes	strain=ATCC 51222	GCA_900167205.1	290054	290054	type	True	89.6089	494	673	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-04 18:46:14,356] [INFO] DFAST Taxonomy check result was written to GCA_934552765.1_ERR7746411_bin.108_genomic.fna/tc_result.tsv
[2023-06-04 18:46:14,357] [INFO] ===== Taxonomy check completed =====
[2023-06-04 18:46:14,357] [INFO] ===== Start completeness check using CheckM =====
[2023-06-04 18:46:14,357] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg12c080d7-37c0-448f-9415-2325c78baf1b/dqc_reference/checkm_data
[2023-06-04 18:46:14,358] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-04 18:46:14,380] [INFO] Task started: CheckM
[2023-06-04 18:46:14,380] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_934552765.1_ERR7746411_bin.108_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_934552765.1_ERR7746411_bin.108_genomic.fna/checkm_input GCA_934552765.1_ERR7746411_bin.108_genomic.fna/checkm_result
[2023-06-04 18:46:36,813] [INFO] Task succeeded: CheckM
[2023-06-04 18:46:36,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-04 18:46:36,834] [INFO] ===== Completeness check finished =====
[2023-06-04 18:46:36,835] [INFO] ===== Start GTDB Search =====
[2023-06-04 18:46:36,835] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_934552765.1_ERR7746411_bin.108_genomic.fna/markers.fasta)
[2023-06-04 18:46:36,835] [INFO] Task started: Blastn
[2023-06-04 18:46:36,836] [INFO] Running command: blastn -query GCA_934552765.1_ERR7746411_bin.108_genomic.fna/markers.fasta -db /var/lib/cwl/stg12c080d7-37c0-448f-9415-2325c78baf1b/dqc_reference/reference_markers_gtdb.fasta -out GCA_934552765.1_ERR7746411_bin.108_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-04 18:46:37,890] [INFO] Task succeeded: Blastn
[2023-06-04 18:46:37,895] [INFO] Selected 11 target genomes.
[2023-06-04 18:46:37,895] [INFO] Target genome list was writen to GCA_934552765.1_ERR7746411_bin.108_genomic.fna/target_genomes_gtdb.txt
[2023-06-04 18:46:37,961] [INFO] Task started: fastANI
[2023-06-04 18:46:37,961] [INFO] Running command: fastANI --query /var/lib/cwl/stgac99241f-facc-4daa-a168-0fd9c0d27131/GCA_934552765.1_ERR7746411_bin.108_genomic.fna.gz --refList GCA_934552765.1_ERR7746411_bin.108_genomic.fna/target_genomes_gtdb.txt --output GCA_934552765.1_ERR7746411_bin.108_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-04 18:46:42,476] [INFO] Task succeeded: fastANI
[2023-06-04 18:46:42,490] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-04 18:46:42,490] [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_900539325.1	s__Eubacterium_R sp900539325	97.2986	573	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.44	97.34	0.90	0.87	4	conclusive
GCF_900167205.1	s__Eubacterium_R coprostanoligenes	89.5641	496	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	98.02	97.98	0.90	0.89	4	-
GCA_900766895.1	s__Eubacterium_R sp900766895	81.0935	310	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900772705.1	s__Eubacterium_R sp900772705	80.2112	194	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900539165.1	s__Eubacterium_R sp900539165	79.8352	293	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	99.98	99.98	0.94	0.94	2	-
GCA_900542875.1	s__Eubacterium_R sp900542875	79.5448	257	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	97.37	97.10	0.91	0.86	6	-
GCA_017514345.1	s__Eubacterium_R sp017514345	77.7295	129	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017445905.1	s__Eubacterium_R sp017445905	77.5959	128	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015065505.1	s__Eubacterium_R sp015065505	77.4616	148	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017543415.1	s__Eubacterium_R sp017543415	76.7359	69	673	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Oscillospirales;f__Acutalibacteraceae;g__Eubacterium_R	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-04 18:46:42,493] [INFO] GTDB search result was written to GCA_934552765.1_ERR7746411_bin.108_genomic.fna/result_gtdb.tsv
[2023-06-04 18:46:42,493] [INFO] ===== GTDB Search completed =====
[2023-06-04 18:46:42,496] [INFO] DFAST_QC result json was written to GCA_934552765.1_ERR7746411_bin.108_genomic.fna/dqc_result.json
[2023-06-04 18:46:42,496] [INFO] DFAST_QC completed!
[2023-06-04 18:46:42,496] [INFO] Total running time: 0h0m48s