[2024-01-25 20:12:05,858] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:12:05,859] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:12:05,859] [INFO] DQC Reference Directory: /var/lib/cwl/stgc097ffea-bbc6-4512-b3b1-37d7211536b5/dqc_reference
[2024-01-25 20:12:07,074] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:12:07,075] [INFO] Task started: Prodigal
[2024-01-25 20:12:07,075] [INFO] Running command: gunzip -c /var/lib/cwl/stg85f5ae88-59f9-4fc8-b5a5-2d8908451687/GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna.gz | prodigal -d GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/cds.fna -a GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:12:08,704] [INFO] Task succeeded: Prodigal
[2024-01-25 20:12:08,705] [INFO] Task started: HMMsearch
[2024-01-25 20:12:08,705] [INFO] Running command: hmmsearch --tblout GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc097ffea-bbc6-4512-b3b1-37d7211536b5/dqc_reference/reference_markers.hmm GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:12:08,861] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:12:08,862] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg85f5ae88-59f9-4fc8-b5a5-2d8908451687/GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna.gz]
[2024-01-25 20:12:08,878] [INFO] Query marker FASTA was written to GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/markers.fasta
[2024-01-25 20:12:08,878] [INFO] Task started: Blastn
[2024-01-25 20:12:08,878] [INFO] Running command: blastn -query GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc097ffea-bbc6-4512-b3b1-37d7211536b5/dqc_reference/reference_markers.fasta -out GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:09,367] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:09,370] [INFO] Selected 8 target genomes.
[2024-01-25 20:12:09,370] [INFO] Target genome list was writen to GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-25 20:12:09,402] [INFO] Task started: fastANI
[2024-01-25 20:12:09,402] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f5ae88-59f9-4fc8-b5a5-2d8908451687/GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna.gz --refList GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:12:11,536] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:11,536] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc097ffea-bbc6-4512-b3b1-37d7211536b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:12:11,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc097ffea-bbc6-4512-b3b1-37d7211536b5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:12:11,540] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:12:11,540] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:12:11,540] [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
Mycoplasmopsis agassizii	strain=PS6	GCA_002272945.1	33922	33922	type	True	99.9937	404	405	95	conclusive
--------------------------------------------------------------------------------
[2024-01-25 20:12:11,541] [INFO] DFAST Taxonomy check result was written to GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-25 20:12:11,542] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:12:11,542] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:12:11,542] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc097ffea-bbc6-4512-b3b1-37d7211536b5/dqc_reference/checkm_data
[2024-01-25 20:12:11,543] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:12:11,558] [INFO] Task started: CheckM
[2024-01-25 20:12:11,558] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/checkm_input GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/checkm_result
[2024-01-25 20:12:23,647] [INFO] Task succeeded: CheckM
[2024-01-25 20:12:23,648] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:12:23,714] [INFO] ===== Completeness check finished =====
[2024-01-25 20:12:23,714] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:12:23,714] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-25 20:12:23,714] [INFO] Task started: Blastn
[2024-01-25 20:12:23,715] [INFO] Running command: blastn -query GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stgc097ffea-bbc6-4512-b3b1-37d7211536b5/dqc_reference/reference_markers_gtdb.fasta -out GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:12:24,371] [INFO] Task succeeded: Blastn
[2024-01-25 20:12:24,373] [INFO] Selected 16 target genomes.
[2024-01-25 20:12:24,373] [INFO] Target genome list was writen to GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:12:24,385] [INFO] Task started: fastANI
[2024-01-25 20:12:24,385] [INFO] Running command: fastANI --query /var/lib/cwl/stg85f5ae88-59f9-4fc8-b5a5-2d8908451687/GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna.gz --refList GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:12:28,893] [INFO] Task succeeded: fastANI
[2024-01-25 20:12:28,896] [INFO] Found 2 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:12:28,896] [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_900176265.1	s__Mycoplasmopsis_B agassizii	100.0	403	405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_B	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_002276225.1	s__Mycoplasmopsis_B agassizii_A	92.3697	347	405	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:12:28,898] [INFO] GTDB search result was written to GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-25 20:12:28,898] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:12:28,900] [INFO] DFAST_QC result json was written to GCF_900176265.1_IMG-taxon_2585428149_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-25 20:12:28,900] [INFO] DFAST_QC completed!
[2024-01-25 20:12:28,900] [INFO] Total running time: 0h0m23s