[2024-01-24 13:27:42,095] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:42,096] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:42,097] [INFO] DQC Reference Directory: /var/lib/cwl/stg88fdf620-5a6f-4f7b-b183-299c4cc1da68/dqc_reference
[2024-01-24 13:27:43,353] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:43,354] [INFO] Task started: Prodigal
[2024-01-24 13:27:43,354] [INFO] Running command: gunzip -c /var/lib/cwl/stg4883f264-399b-4b93-aa69-b5d050d6c8d9/GCF_007859615.1_ASM785961v1_genomic.fna.gz | prodigal -d GCF_007859615.1_ASM785961v1_genomic.fna/cds.fna -a GCF_007859615.1_ASM785961v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:44,874] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:44,875] [INFO] Task started: HMMsearch
[2024-01-24 13:27:44,875] [INFO] Running command: hmmsearch --tblout GCF_007859615.1_ASM785961v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg88fdf620-5a6f-4f7b-b183-299c4cc1da68/dqc_reference/reference_markers.hmm GCF_007859615.1_ASM785961v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:45,075] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:45,077] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg4883f264-399b-4b93-aa69-b5d050d6c8d9/GCF_007859615.1_ASM785961v1_genomic.fna.gz]
[2024-01-24 13:27:45,092] [INFO] Query marker FASTA was written to GCF_007859615.1_ASM785961v1_genomic.fna/markers.fasta
[2024-01-24 13:27:45,093] [INFO] Task started: Blastn
[2024-01-24 13:27:45,093] [INFO] Running command: blastn -query GCF_007859615.1_ASM785961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88fdf620-5a6f-4f7b-b183-299c4cc1da68/dqc_reference/reference_markers.fasta -out GCF_007859615.1_ASM785961v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:27:45,674] [INFO] Task succeeded: Blastn
[2024-01-24 13:27:45,678] [INFO] Selected 14 target genomes.
[2024-01-24 13:27:45,678] [INFO] Target genome list was writen to GCF_007859615.1_ASM785961v1_genomic.fna/target_genomes.txt
[2024-01-24 13:27:45,727] [INFO] Task started: fastANI
[2024-01-24 13:27:45,727] [INFO] Running command: fastANI --query /var/lib/cwl/stg4883f264-399b-4b93-aa69-b5d050d6c8d9/GCF_007859615.1_ASM785961v1_genomic.fna.gz --refList GCF_007859615.1_ASM785961v1_genomic.fna/target_genomes.txt --output GCF_007859615.1_ASM785961v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:27:48,307] [INFO] Task succeeded: fastANI
[2024-01-24 13:27:48,307] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg88fdf620-5a6f-4f7b-b183-299c4cc1da68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:27:48,308] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg88fdf620-5a6f-4f7b-b183-299c4cc1da68/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:27:48,313] [INFO] Found 4 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:27:48,313] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:27:48,313] [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 anatis	strain=NCTC 10156	GCA_003285065.1	171279	171279	type	True	84.3359	235	319	95	below_threshold
Mycoplasmopsis anatis	strain=1340	GCA_000221305.2	171279	171279	type	True	84.3141	212	319	95	below_threshold
Mycoplasmopsis anatis	strain=NCTC10156	GCA_900660655.1	171279	171279	type	True	84.2577	237	319	95	below_threshold
Mycoplasmopsis edwardii	strain=NCTC10132	GCA_900476105.1	53558	53558	type	True	78.0248	65	319	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:27:48,315] [INFO] DFAST Taxonomy check result was written to GCF_007859615.1_ASM785961v1_genomic.fna/tc_result.tsv
[2024-01-24 13:27:48,315] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:27:48,315] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:27:48,315] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg88fdf620-5a6f-4f7b-b183-299c4cc1da68/dqc_reference/checkm_data
[2024-01-24 13:27:48,316] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:27:48,333] [INFO] Task started: CheckM
[2024-01-24 13:27:48,333] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007859615.1_ASM785961v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007859615.1_ASM785961v1_genomic.fna/checkm_input GCF_007859615.1_ASM785961v1_genomic.fna/checkm_result
[2024-01-24 13:28:02,669] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:02,670] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:02,687] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:02,688] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:02,688] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007859615.1_ASM785961v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:02,688] [INFO] Task started: Blastn
[2024-01-24 13:28:02,689] [INFO] Running command: blastn -query GCF_007859615.1_ASM785961v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg88fdf620-5a6f-4f7b-b183-299c4cc1da68/dqc_reference/reference_markers_gtdb.fasta -out GCF_007859615.1_ASM785961v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:03,432] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:03,436] [INFO] Selected 15 target genomes.
[2024-01-24 13:28:03,436] [INFO] Target genome list was writen to GCF_007859615.1_ASM785961v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:03,447] [INFO] Task started: fastANI
[2024-01-24 13:28:03,448] [INFO] Running command: fastANI --query /var/lib/cwl/stg4883f264-399b-4b93-aa69-b5d050d6c8d9/GCF_007859615.1_ASM785961v1_genomic.fna.gz --refList GCF_007859615.1_ASM785961v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007859615.1_ASM785961v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:05,960] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:05,970] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:05,970] [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_007859615.1	s__Mycoplasmopsis_A anserisalpingitidis	100.0	316	319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	97.47	97.47	0.93	0.93	2	conclusive
GCF_007858495.1	s__Mycoplasmopsis_A anserisalpingitidis_A	93.1346	276	319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900660655.1	s__Mycoplasmopsis_A anatis	84.2361	237	319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.97	99.95	1.00	1.00	3	-
GCF_900476105.1	s__Mycoplasmopsis_A edwardii	78.1772	65	319	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:05,976] [INFO] GTDB search result was written to GCF_007859615.1_ASM785961v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:05,978] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:05,981] [INFO] DFAST_QC result json was written to GCF_007859615.1_ASM785961v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:05,982] [INFO] DFAST_QC completed!
[2024-01-24 13:28:05,982] [INFO] Total running time: 0h0m24s