[2024-01-24 12:21:56,547] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:56,549] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:56,550] [INFO] DQC Reference Directory: /var/lib/cwl/stgc1811be3-c60c-4437-b0c4-3f10b910cd65/dqc_reference
[2024-01-24 12:21:57,818] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:57,819] [INFO] Task started: Prodigal
[2024-01-24 12:21:57,819] [INFO] Running command: gunzip -c /var/lib/cwl/stg3047fed8-2fd0-4bda-80dc-8eceb561daed/GCF_024498275.1_ASM2449827v1_genomic.fna.gz | prodigal -d GCF_024498275.1_ASM2449827v1_genomic.fna/cds.fna -a GCF_024498275.1_ASM2449827v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:59,905] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:59,906] [INFO] Task started: HMMsearch
[2024-01-24 12:21:59,906] [INFO] Running command: hmmsearch --tblout GCF_024498275.1_ASM2449827v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc1811be3-c60c-4437-b0c4-3f10b910cd65/dqc_reference/reference_markers.hmm GCF_024498275.1_ASM2449827v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:22:00,271] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:22:00,272] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3047fed8-2fd0-4bda-80dc-8eceb561daed/GCF_024498275.1_ASM2449827v1_genomic.fna.gz]
[2024-01-24 12:22:00,292] [INFO] Query marker FASTA was written to GCF_024498275.1_ASM2449827v1_genomic.fna/markers.fasta
[2024-01-24 12:22:00,298] [INFO] Task started: Blastn
[2024-01-24 12:22:00,299] [INFO] Running command: blastn -query GCF_024498275.1_ASM2449827v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1811be3-c60c-4437-b0c4-3f10b910cd65/dqc_reference/reference_markers.fasta -out GCF_024498275.1_ASM2449827v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:00,935] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:00,939] [INFO] Selected 8 target genomes.
[2024-01-24 12:22:00,940] [INFO] Target genome list was writen to GCF_024498275.1_ASM2449827v1_genomic.fna/target_genomes.txt
[2024-01-24 12:22:00,986] [INFO] Task started: fastANI
[2024-01-24 12:22:00,986] [INFO] Running command: fastANI --query /var/lib/cwl/stg3047fed8-2fd0-4bda-80dc-8eceb561daed/GCF_024498275.1_ASM2449827v1_genomic.fna.gz --refList GCF_024498275.1_ASM2449827v1_genomic.fna/target_genomes.txt --output GCF_024498275.1_ASM2449827v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:22:02,951] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:02,952] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc1811be3-c60c-4437-b0c4-3f10b910cd65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:22:02,952] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc1811be3-c60c-4437-b0c4-3f10b910cd65/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:22:02,956] [INFO] Found 1 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:22:02,956] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:22:02,956] [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
Mycoplasmoides fastidiosum	strain=4822	GCA_024498275.1	92758	92758	type	True	100.0	407	407	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 12:22:02,957] [INFO] DFAST Taxonomy check result was written to GCF_024498275.1_ASM2449827v1_genomic.fna/tc_result.tsv
[2024-01-24 12:22:02,958] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:22:02,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:22:02,958] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc1811be3-c60c-4437-b0c4-3f10b910cd65/dqc_reference/checkm_data
[2024-01-24 12:22:02,959] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:22:02,973] [INFO] Task started: CheckM
[2024-01-24 12:22:02,973] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_024498275.1_ASM2449827v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_024498275.1_ASM2449827v1_genomic.fna/checkm_input GCF_024498275.1_ASM2449827v1_genomic.fna/checkm_result
[2024-01-24 12:22:20,000] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:20,001] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:20,029] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:20,030] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:20,030] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_024498275.1_ASM2449827v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:20,031] [INFO] Task started: Blastn
[2024-01-24 12:22:20,031] [INFO] Running command: blastn -query GCF_024498275.1_ASM2449827v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc1811be3-c60c-4437-b0c4-3f10b910cd65/dqc_reference/reference_markers_gtdb.fasta -out GCF_024498275.1_ASM2449827v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:20,707] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:20,710] [INFO] Selected 9 target genomes.
[2024-01-24 12:22:20,710] [INFO] Target genome list was writen to GCF_024498275.1_ASM2449827v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:20,746] [INFO] Task started: fastANI
[2024-01-24 12:22:20,746] [INFO] Running command: fastANI --query /var/lib/cwl/stg3047fed8-2fd0-4bda-80dc-8eceb561daed/GCF_024498275.1_ASM2449827v1_genomic.fna.gz --refList GCF_024498275.1_ASM2449827v1_genomic.fna/target_genomes_gtdb.txt --output GCF_024498275.1_ASM2449827v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:24,134] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:24,136] [INFO] Found 0 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:22:24,136] [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
--------------------------------------------------------------------------------
[2024-01-24 12:22:24,138] [INFO] GTDB search result was written to GCF_024498275.1_ASM2449827v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:24,138] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:24,140] [INFO] DFAST_QC result json was written to GCF_024498275.1_ASM2449827v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:24,140] [INFO] DFAST_QC completed!
[2024-01-24 12:22:24,140] [INFO] Total running time: 0h0m28s