[2024-01-24 12:28:34,791] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:28:34,794] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:28:34,795] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ad6a742-4531-446f-a5a6-416a3629d627/dqc_reference
[2024-01-24 12:28:35,992] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:28:35,995] [INFO] Task started: Prodigal
[2024-01-24 12:28:35,996] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ea27628-4d15-4736-826c-075b5871ee69/GCF_028912405.1_ASM2891240v1_genomic.fna.gz | prodigal -d GCF_028912405.1_ASM2891240v1_genomic.fna/cds.fna -a GCF_028912405.1_ASM2891240v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:28:42,380] [INFO] Task succeeded: Prodigal
[2024-01-24 12:28:42,381] [INFO] Task started: HMMsearch
[2024-01-24 12:28:42,381] [INFO] Running command: hmmsearch --tblout GCF_028912405.1_ASM2891240v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ad6a742-4531-446f-a5a6-416a3629d627/dqc_reference/reference_markers.hmm GCF_028912405.1_ASM2891240v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:28:42,571] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:28:42,572] [WARNING] Found 2/6 markers. [/var/lib/cwl/stg0ea27628-4d15-4736-826c-075b5871ee69/GCF_028912405.1_ASM2891240v1_genomic.fna.gz]
[2024-01-24 12:28:42,594] [INFO] Query marker FASTA was written to GCF_028912405.1_ASM2891240v1_genomic.fna/markers.fasta
[2024-01-24 12:28:42,595] [INFO] Task started: Blastn
[2024-01-24 12:28:42,595] [INFO] Running command: blastn -query GCF_028912405.1_ASM2891240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad6a742-4531-446f-a5a6-416a3629d627/dqc_reference/reference_markers.fasta -out GCF_028912405.1_ASM2891240v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:28:43,101] [INFO] Task succeeded: Blastn
[2024-01-24 12:28:43,106] [INFO] Selected 5 target genomes.
[2024-01-24 12:28:43,106] [INFO] Target genome list was writen to GCF_028912405.1_ASM2891240v1_genomic.fna/target_genomes.txt
[2024-01-24 12:28:43,166] [INFO] Task started: fastANI
[2024-01-24 12:28:43,166] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea27628-4d15-4736-826c-075b5871ee69/GCF_028912405.1_ASM2891240v1_genomic.fna.gz --refList GCF_028912405.1_ASM2891240v1_genomic.fna/target_genomes.txt --output GCF_028912405.1_ASM2891240v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:28:45,187] [INFO] Task succeeded: fastANI
[2024-01-24 12:28:45,188] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ad6a742-4531-446f-a5a6-416a3629d627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:28:45,189] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ad6a742-4531-446f-a5a6-416a3629d627/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:28:45,193] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:28:45,193] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:28:45,193] [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
Methanogenium cariaci	strain=JCM 10550	GCA_001315945.1	2197	2197	type	True	82.2339	465	744	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:28:45,196] [INFO] DFAST Taxonomy check result was written to GCF_028912405.1_ASM2891240v1_genomic.fna/tc_result.tsv
[2024-01-24 12:28:45,196] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:28:45,196] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:28:45,196] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ad6a742-4531-446f-a5a6-416a3629d627/dqc_reference/checkm_data
[2024-01-24 12:28:45,197] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:28:45,225] [INFO] Task started: CheckM
[2024-01-24 12:28:45,225] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028912405.1_ASM2891240v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028912405.1_ASM2891240v1_genomic.fna/checkm_input GCF_028912405.1_ASM2891240v1_genomic.fna/checkm_result
[2024-01-24 12:29:10,246] [INFO] Task succeeded: CheckM
[2024-01-24 12:29:10,248] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 75.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:29:10,269] [INFO] ===== Completeness check finished =====
[2024-01-24 12:29:10,269] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:29:10,269] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028912405.1_ASM2891240v1_genomic.fna/markers.fasta)
[2024-01-24 12:29:10,270] [INFO] Task started: Blastn
[2024-01-24 12:29:10,270] [INFO] Running command: blastn -query GCF_028912405.1_ASM2891240v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ad6a742-4531-446f-a5a6-416a3629d627/dqc_reference/reference_markers_gtdb.fasta -out GCF_028912405.1_ASM2891240v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:29:10,789] [INFO] Task succeeded: Blastn
[2024-01-24 12:29:10,793] [INFO] Selected 6 target genomes.
[2024-01-24 12:29:10,793] [INFO] Target genome list was writen to GCF_028912405.1_ASM2891240v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:29:10,826] [INFO] Task started: fastANI
[2024-01-24 12:29:10,827] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ea27628-4d15-4736-826c-075b5871ee69/GCF_028912405.1_ASM2891240v1_genomic.fna.gz --refList GCF_028912405.1_ASM2891240v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028912405.1_ASM2891240v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:29:13,281] [INFO] Task succeeded: fastANI
[2024-01-24 12:29:13,288] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:29:13,289] [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_009914725.1	s__Methanogenium sp009914725	83.8526	431	744	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001315945.1	s__Methanogenium cariaci	82.2339	465	744	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016841485.1	s__Methanogenium sp016841485	77.7541	73	744	d__Archaea;p__Halobacteriota;c__Methanomicrobia;o__Methanomicrobiales;f__Methanomicrobiaceae;g__Methanogenium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:29:13,291] [INFO] GTDB search result was written to GCF_028912405.1_ASM2891240v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:29:13,292] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:29:13,294] [INFO] DFAST_QC result json was written to GCF_028912405.1_ASM2891240v1_genomic.fna/dqc_result.json
[2024-01-24 12:29:13,294] [INFO] DFAST_QC completed!
[2024-01-24 12:29:13,294] [INFO] Total running time: 0h0m39s