[2024-01-24 13:57:56,316] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:57:56,317] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:57:56,318] [INFO] DQC Reference Directory: /var/lib/cwl/stga301d8ab-1387-411f-b5cc-d159c4ad5da3/dqc_reference
[2024-01-24 13:57:57,696] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:57:57,697] [INFO] Task started: Prodigal
[2024-01-24 13:57:57,697] [INFO] Running command: gunzip -c /var/lib/cwl/stg3400d1af-8b78-4f23-80e0-9cb9d581f0a1/GCF_004362335.1_ASM436233v1_genomic.fna.gz | prodigal -d GCF_004362335.1_ASM436233v1_genomic.fna/cds.fna -a GCF_004362335.1_ASM436233v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:57:59,284] [INFO] Task succeeded: Prodigal
[2024-01-24 13:57:59,285] [INFO] Task started: HMMsearch
[2024-01-24 13:57:59,285] [INFO] Running command: hmmsearch --tblout GCF_004362335.1_ASM436233v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga301d8ab-1387-411f-b5cc-d159c4ad5da3/dqc_reference/reference_markers.hmm GCF_004362335.1_ASM436233v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:57:59,500] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:57:59,504] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3400d1af-8b78-4f23-80e0-9cb9d581f0a1/GCF_004362335.1_ASM436233v1_genomic.fna.gz]
[2024-01-24 13:57:59,523] [INFO] Query marker FASTA was written to GCF_004362335.1_ASM436233v1_genomic.fna/markers.fasta
[2024-01-24 13:57:59,524] [INFO] Task started: Blastn
[2024-01-24 13:57:59,524] [INFO] Running command: blastn -query GCF_004362335.1_ASM436233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga301d8ab-1387-411f-b5cc-d159c4ad5da3/dqc_reference/reference_markers.fasta -out GCF_004362335.1_ASM436233v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:00,058] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:00,063] [INFO] Selected 16 target genomes.
[2024-01-24 13:58:00,064] [INFO] Target genome list was writen to GCF_004362335.1_ASM436233v1_genomic.fna/target_genomes.txt
[2024-01-24 13:58:00,085] [INFO] Task started: fastANI
[2024-01-24 13:58:00,085] [INFO] Running command: fastANI --query /var/lib/cwl/stg3400d1af-8b78-4f23-80e0-9cb9d581f0a1/GCF_004362335.1_ASM436233v1_genomic.fna.gz --refList GCF_004362335.1_ASM436233v1_genomic.fna/target_genomes.txt --output GCF_004362335.1_ASM436233v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:58:03,881] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:03,882] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga301d8ab-1387-411f-b5cc-d159c4ad5da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:58:03,882] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga301d8ab-1387-411f-b5cc-d159c4ad5da3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:58:03,886] [INFO] Found 2 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:58:03,886] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:58:03,887] [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
Mycoplasma testudineum	strain=ATCC 700618	GCA_004362335.1	244584	244584	type	True	100.0	308	309	95	conclusive
Mycoplasma testudineum	strain=BH29	GCA_002245785.1	244584	244584	type	True	99.9909	300	309	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 13:58:03,888] [INFO] DFAST Taxonomy check result was written to GCF_004362335.1_ASM436233v1_genomic.fna/tc_result.tsv
[2024-01-24 13:58:03,889] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:58:03,889] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:58:03,889] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga301d8ab-1387-411f-b5cc-d159c4ad5da3/dqc_reference/checkm_data
[2024-01-24 13:58:03,890] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:58:03,904] [INFO] Task started: CheckM
[2024-01-24 13:58:03,904] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004362335.1_ASM436233v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004362335.1_ASM436233v1_genomic.fna/checkm_input GCF_004362335.1_ASM436233v1_genomic.fna/checkm_result
[2024-01-24 13:58:17,902] [INFO] Task succeeded: CheckM
[2024-01-24 13:58:17,903] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:58:17,918] [INFO] ===== Completeness check finished =====
[2024-01-24 13:58:17,919] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:58:17,919] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004362335.1_ASM436233v1_genomic.fna/markers.fasta)
[2024-01-24 13:58:17,920] [INFO] Task started: Blastn
[2024-01-24 13:58:17,920] [INFO] Running command: blastn -query GCF_004362335.1_ASM436233v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga301d8ab-1387-411f-b5cc-d159c4ad5da3/dqc_reference/reference_markers_gtdb.fasta -out GCF_004362335.1_ASM436233v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:58:18,377] [INFO] Task succeeded: Blastn
[2024-01-24 13:58:18,380] [INFO] Selected 15 target genomes.
[2024-01-24 13:58:18,380] [INFO] Target genome list was writen to GCF_004362335.1_ASM436233v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:58:18,392] [INFO] Task started: fastANI
[2024-01-24 13:58:18,392] [INFO] Running command: fastANI --query /var/lib/cwl/stg3400d1af-8b78-4f23-80e0-9cb9d581f0a1/GCF_004362335.1_ASM436233v1_genomic.fna.gz --refList GCF_004362335.1_ASM436233v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004362335.1_ASM436233v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:58:21,313] [INFO] Task succeeded: fastANI
[2024-01-24 13:58:21,316] [INFO] Found 1 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:58:21,316] [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_002245785.1	s__Mycoplasmopsis_B testudinea	99.9909	300	309	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
--------------------------------------------------------------------------------
[2024-01-24 13:58:21,317] [INFO] GTDB search result was written to GCF_004362335.1_ASM436233v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:58:21,318] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:58:21,320] [INFO] DFAST_QC result json was written to GCF_004362335.1_ASM436233v1_genomic.fna/dqc_result.json
[2024-01-24 13:58:21,320] [INFO] DFAST_QC completed!
[2024-01-24 13:58:21,320] [INFO] Total running time: 0h0m25s