[2024-01-24 11:44:05,458] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:05,460] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:05,460] [INFO] DQC Reference Directory: /var/lib/cwl/stga67a3a76-35f2-48fe-a1f0-1ff2b31cddc5/dqc_reference
[2024-01-24 11:44:08,838] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:08,839] [INFO] Task started: Prodigal
[2024-01-24 11:44:08,840] [INFO] Running command: gunzip -c /var/lib/cwl/stg2687d251-a89b-4106-940f-19d008479cde/GCF_000815065.1_ASM81506v1_genomic.fna.gz | prodigal -d GCF_000815065.1_ASM81506v1_genomic.fna/cds.fna -a GCF_000815065.1_ASM81506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:10,206] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:10,206] [INFO] Task started: HMMsearch
[2024-01-24 11:44:10,206] [INFO] Running command: hmmsearch --tblout GCF_000815065.1_ASM81506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga67a3a76-35f2-48fe-a1f0-1ff2b31cddc5/dqc_reference/reference_markers.hmm GCF_000815065.1_ASM81506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:10,478] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:10,480] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg2687d251-a89b-4106-940f-19d008479cde/GCF_000815065.1_ASM81506v1_genomic.fna.gz]
[2024-01-24 11:44:10,502] [INFO] Query marker FASTA was written to GCF_000815065.1_ASM81506v1_genomic.fna/markers.fasta
[2024-01-24 11:44:10,503] [INFO] Task started: Blastn
[2024-01-24 11:44:10,503] [INFO] Running command: blastn -query GCF_000815065.1_ASM81506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga67a3a76-35f2-48fe-a1f0-1ff2b31cddc5/dqc_reference/reference_markers.fasta -out GCF_000815065.1_ASM81506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:14,811] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:14,814] [INFO] Selected 8 target genomes.
[2024-01-24 11:44:14,815] [INFO] Target genome list was writen to GCF_000815065.1_ASM81506v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:14,920] [INFO] Task started: fastANI
[2024-01-24 11:44:14,920] [INFO] Running command: fastANI --query /var/lib/cwl/stg2687d251-a89b-4106-940f-19d008479cde/GCF_000815065.1_ASM81506v1_genomic.fna.gz --refList GCF_000815065.1_ASM81506v1_genomic.fna/target_genomes.txt --output GCF_000815065.1_ASM81506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:16,704] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:16,705] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga67a3a76-35f2-48fe-a1f0-1ff2b31cddc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:16,706] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga67a3a76-35f2-48fe-a1f0-1ff2b31cddc5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:16,715] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:16,715] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:16,716] [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
Mesomycoplasma flocculare	strain=Ms42	GCA_000815065.1	2128	2128	type	True	100.0	258	259	95	conclusive
Mesomycoplasma hyopneumoniae	strain=J	GCA_000008205.1	2099	2099	type	True	82.0711	185	259	95	below_threshold
Mesomycoplasma dispar	strain=ATCC 27140	GCA_000941075.1	86660	86660	type	True	80.3275	176	259	95	below_threshold
Mesomycoplasma dispar	strain=NCTC10125	GCA_900660505.1	86660	86660	type	True	80.2926	175	259	95	below_threshold
Mesomycoplasma ovipneumoniae	strain=ATCC 29419	GCA_001951355.1	29562	29562	suspected-type	True	78.9073	117	259	95	below_threshold
Mesomycoplasma ovipneumoniae	strain=Y98	GCA_001715085.1	29562	29562	suspected-type	True	78.898	112	259	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:16,717] [INFO] DFAST Taxonomy check result was written to GCF_000815065.1_ASM81506v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:16,717] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:16,718] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:16,718] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga67a3a76-35f2-48fe-a1f0-1ff2b31cddc5/dqc_reference/checkm_data
[2024-01-24 11:44:16,719] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:16,733] [INFO] Task started: CheckM
[2024-01-24 11:44:16,733] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000815065.1_ASM81506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000815065.1_ASM81506v1_genomic.fna/checkm_input GCF_000815065.1_ASM81506v1_genomic.fna/checkm_result
[2024-01-24 11:44:35,698] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:35,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,715] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:35,716] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:35,716] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000815065.1_ASM81506v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:35,717] [INFO] Task started: Blastn
[2024-01-24 11:44:35,718] [INFO] Running command: blastn -query GCF_000815065.1_ASM81506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga67a3a76-35f2-48fe-a1f0-1ff2b31cddc5/dqc_reference/reference_markers_gtdb.fasta -out GCF_000815065.1_ASM81506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:36,551] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:36,554] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:36,554] [INFO] Target genome list was writen to GCF_000815065.1_ASM81506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:36,565] [INFO] Task started: fastANI
[2024-01-24 11:44:36,565] [INFO] Running command: fastANI --query /var/lib/cwl/stg2687d251-a89b-4106-940f-19d008479cde/GCF_000815065.1_ASM81506v1_genomic.fna.gz --refList GCF_000815065.1_ASM81506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000815065.1_ASM81506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:39,630] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:39,642] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:39,642] [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_000815065.1	s__Mesomycoplasma flocculare	100.0	257	259	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	99.48	99.31	0.98	0.96	9	conclusive
GCF_000008205.1	s__Mesomycoplasma hyopneumoniae	82.0711	185	259	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	98.57	98.32	0.96	0.93	23	-
GCF_000941075.1	s__Mesomycoplasma dispar	80.2743	177	259	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	99.26	98.51	0.97	0.95	3	-
GCF_000218525.1	s__Mesomycoplasma ovipneumoniae_A	79.2475	119	259	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	97.12	95.45	0.91	0.88	8	-
GCF_001951355.1	s__Mesomycoplasma ovipneumoniae	78.9465	116	259	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	97.10	95.23	0.91	0.73	7	-
GCF_015708155.1	s__Mesomycoplasma sp015708155	77.5652	77	259	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:39,644] [INFO] GTDB search result was written to GCF_000815065.1_ASM81506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:39,645] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:39,649] [INFO] DFAST_QC result json was written to GCF_000815065.1_ASM81506v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:39,649] [INFO] DFAST_QC completed!
[2024-01-24 11:44:39,649] [INFO] Total running time: 0h0m34s