[2024-01-24 13:22:40,782] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:22:40,783] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:22:40,784] [INFO] DQC Reference Directory: /var/lib/cwl/stg3f6b3f1d-c823-4af2-946b-0335b3fbd8f2/dqc_reference
[2024-01-24 13:22:42,207] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:22:42,208] [INFO] Task started: Prodigal
[2024-01-24 13:22:42,208] [INFO] Running command: gunzip -c /var/lib/cwl/stge57cad80-1ede-46ab-9666-c48249251185/GCF_006491995.1_ASM649199v1_genomic.fna.gz | prodigal -d GCF_006491995.1_ASM649199v1_genomic.fna/cds.fna -a GCF_006491995.1_ASM649199v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:22:43,575] [INFO] Task succeeded: Prodigal
[2024-01-24 13:22:43,575] [INFO] Task started: HMMsearch
[2024-01-24 13:22:43,575] [INFO] Running command: hmmsearch --tblout GCF_006491995.1_ASM649199v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg3f6b3f1d-c823-4af2-946b-0335b3fbd8f2/dqc_reference/reference_markers.hmm GCF_006491995.1_ASM649199v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:22:43,765] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:22:43,766] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge57cad80-1ede-46ab-9666-c48249251185/GCF_006491995.1_ASM649199v1_genomic.fna.gz]
[2024-01-24 13:22:43,781] [INFO] Query marker FASTA was written to GCF_006491995.1_ASM649199v1_genomic.fna/markers.fasta
[2024-01-24 13:22:43,781] [INFO] Task started: Blastn
[2024-01-24 13:22:43,781] [INFO] Running command: blastn -query GCF_006491995.1_ASM649199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f6b3f1d-c823-4af2-946b-0335b3fbd8f2/dqc_reference/reference_markers.fasta -out GCF_006491995.1_ASM649199v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:44,434] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:44,438] [INFO] Selected 8 target genomes.
[2024-01-24 13:22:44,439] [INFO] Target genome list was writen to GCF_006491995.1_ASM649199v1_genomic.fna/target_genomes.txt
[2024-01-24 13:22:44,443] [INFO] Task started: fastANI
[2024-01-24 13:22:44,443] [INFO] Running command: fastANI --query /var/lib/cwl/stge57cad80-1ede-46ab-9666-c48249251185/GCF_006491995.1_ASM649199v1_genomic.fna.gz --refList GCF_006491995.1_ASM649199v1_genomic.fna/target_genomes.txt --output GCF_006491995.1_ASM649199v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:22:45,742] [INFO] Task succeeded: fastANI
[2024-01-24 13:22:45,742] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg3f6b3f1d-c823-4af2-946b-0335b3fbd8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:22:45,743] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg3f6b3f1d-c823-4af2-946b-0335b3fbd8f2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:22:45,749] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:22:45,749] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:22:45,749] [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 struthionis	strain=237IA	GCA_003855455.1	538220	538220	type	True	79.1609	78	230	95	below_threshold
Metamycoplasma falconis	strain=ATCC 51372	GCA_006385795.1	92403	92403	type	True	78.9969	70	230	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:22:45,751] [INFO] DFAST Taxonomy check result was written to GCF_006491995.1_ASM649199v1_genomic.fna/tc_result.tsv
[2024-01-24 13:22:45,752] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:22:45,753] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:22:45,753] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg3f6b3f1d-c823-4af2-946b-0335b3fbd8f2/dqc_reference/checkm_data
[2024-01-24 13:22:45,755] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:22:45,768] [INFO] Task started: CheckM
[2024-01-24 13:22:45,769] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006491995.1_ASM649199v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006491995.1_ASM649199v1_genomic.fna/checkm_input GCF_006491995.1_ASM649199v1_genomic.fna/checkm_result
[2024-01-24 13:22:58,331] [INFO] Task succeeded: CheckM
[2024-01-24 13:22:58,333] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:22:58,349] [INFO] ===== Completeness check finished =====
[2024-01-24 13:22:58,350] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:22:58,350] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006491995.1_ASM649199v1_genomic.fna/markers.fasta)
[2024-01-24 13:22:58,350] [INFO] Task started: Blastn
[2024-01-24 13:22:58,350] [INFO] Running command: blastn -query GCF_006491995.1_ASM649199v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg3f6b3f1d-c823-4af2-946b-0335b3fbd8f2/dqc_reference/reference_markers_gtdb.fasta -out GCF_006491995.1_ASM649199v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:22:59,074] [INFO] Task succeeded: Blastn
[2024-01-24 13:22:59,077] [INFO] Selected 12 target genomes.
[2024-01-24 13:22:59,078] [INFO] Target genome list was writen to GCF_006491995.1_ASM649199v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:22:59,086] [INFO] Task started: fastANI
[2024-01-24 13:22:59,086] [INFO] Running command: fastANI --query /var/lib/cwl/stge57cad80-1ede-46ab-9666-c48249251185/GCF_006491995.1_ASM649199v1_genomic.fna.gz --refList GCF_006491995.1_ASM649199v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006491995.1_ASM649199v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:23:01,524] [INFO] Task succeeded: fastANI
[2024-01-24 13:23:01,531] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:23:01,531] [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_006491995.1	s__Metamycoplasma neophronis	100.0	230	230	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000620005.1	s__Metamycoplasma spumans	80.3789	118	230	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003855455.1	s__Metamycoplasma struthionis	79.1609	78	230	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	98.82	98.82	0.96	0.96	2	-
GCF_006385185.1	s__Metamycoplasma equirhinis	78.2888	70	230	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017116825.1	s__Metamycoplasma enhydrae	78.2443	62	230	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Metamycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:23:01,533] [INFO] GTDB search result was written to GCF_006491995.1_ASM649199v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:23:01,534] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:23:01,537] [INFO] DFAST_QC result json was written to GCF_006491995.1_ASM649199v1_genomic.fna/dqc_result.json
[2024-01-24 13:23:01,537] [INFO] DFAST_QC completed!
[2024-01-24 13:23:01,537] [INFO] Total running time: 0h0m21s