[2024-01-24 12:13:42,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:13:42,798] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:13:42,798] [INFO] DQC Reference Directory: /var/lib/cwl/stg15d42db4-ffd1-49d5-8fa0-037433c98f4d/dqc_reference
[2024-01-24 12:13:44,240] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:13:44,241] [INFO] Task started: Prodigal
[2024-01-24 12:13:44,242] [INFO] Running command: gunzip -c /var/lib/cwl/stge2e263ff-43b8-490a-84a6-3e2283f40b73/GCF_900660505.1_50861_E01-3_genomic.fna.gz | prodigal -d GCF_900660505.1_50861_E01-3_genomic.fna/cds.fna -a GCF_900660505.1_50861_E01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:13:46,194] [INFO] Task succeeded: Prodigal
[2024-01-24 12:13:46,195] [INFO] Task started: HMMsearch
[2024-01-24 12:13:46,195] [INFO] Running command: hmmsearch --tblout GCF_900660505.1_50861_E01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg15d42db4-ffd1-49d5-8fa0-037433c98f4d/dqc_reference/reference_markers.hmm GCF_900660505.1_50861_E01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:13:46,422] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:13:46,424] [WARNING] Found 4/6 markers. [/var/lib/cwl/stge2e263ff-43b8-490a-84a6-3e2283f40b73/GCF_900660505.1_50861_E01-3_genomic.fna.gz]
[2024-01-24 12:13:46,444] [INFO] Query marker FASTA was written to GCF_900660505.1_50861_E01-3_genomic.fna/markers.fasta
[2024-01-24 12:13:46,445] [INFO] Task started: Blastn
[2024-01-24 12:13:46,445] [INFO] Running command: blastn -query GCF_900660505.1_50861_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d42db4-ffd1-49d5-8fa0-037433c98f4d/dqc_reference/reference_markers.fasta -out GCF_900660505.1_50861_E01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:13:46,961] [INFO] Task succeeded: Blastn
[2024-01-24 12:13:46,964] [INFO] Selected 9 target genomes.
[2024-01-24 12:13:46,965] [INFO] Target genome list was writen to GCF_900660505.1_50861_E01-3_genomic.fna/target_genomes.txt
[2024-01-24 12:13:47,009] [INFO] Task started: fastANI
[2024-01-24 12:13:47,009] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e263ff-43b8-490a-84a6-3e2283f40b73/GCF_900660505.1_50861_E01-3_genomic.fna.gz --refList GCF_900660505.1_50861_E01-3_genomic.fna/target_genomes.txt --output GCF_900660505.1_50861_E01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:13:49,817] [INFO] Task succeeded: fastANI
[2024-01-24 12:13:49,818] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg15d42db4-ffd1-49d5-8fa0-037433c98f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:13:49,818] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg15d42db4-ffd1-49d5-8fa0-037433c98f4d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:13:49,825] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:13:49,825] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:13:49,825] [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 dispar	strain=NCTC10125	GCA_900660505.1	86660	86660	type	True	100.0	360	361	95	conclusive
Mesomycoplasma dispar	strain=ATCC 27140	GCA_000941075.1	86660	86660	type	True	99.9983	360	361	95	conclusive
Mesomycoplasma flocculare	strain=Ms42	GCA_000815065.1	2128	2128	type	True	80.5472	171	361	95	below_threshold
Mesomycoplasma ovipneumoniae	strain=Y98	GCA_001715085.1	29562	29562	suspected-type	True	80.3525	154	361	95	below_threshold
Mesomycoplasma hyopneumoniae	strain=J	GCA_000008205.1	2099	2099	type	True	80.1719	169	361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:13:49,827] [INFO] DFAST Taxonomy check result was written to GCF_900660505.1_50861_E01-3_genomic.fna/tc_result.tsv
[2024-01-24 12:13:49,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:13:49,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:13:49,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg15d42db4-ffd1-49d5-8fa0-037433c98f4d/dqc_reference/checkm_data
[2024-01-24 12:13:49,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:13:49,844] [INFO] Task started: CheckM
[2024-01-24 12:13:49,844] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660505.1_50861_E01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660505.1_50861_E01-3_genomic.fna/checkm_input GCF_900660505.1_50861_E01-3_genomic.fna/checkm_result
[2024-01-24 12:14:05,974] [INFO] Task succeeded: CheckM
[2024-01-24 12:14:05,975] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:14:06,007] [INFO] ===== Completeness check finished =====
[2024-01-24 12:14:06,007] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:14:06,008] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660505.1_50861_E01-3_genomic.fna/markers.fasta)
[2024-01-24 12:14:06,008] [INFO] Task started: Blastn
[2024-01-24 12:14:06,009] [INFO] Running command: blastn -query GCF_900660505.1_50861_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg15d42db4-ffd1-49d5-8fa0-037433c98f4d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660505.1_50861_E01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:14:06,484] [INFO] Task succeeded: Blastn
[2024-01-24 12:14:06,488] [INFO] Selected 14 target genomes.
[2024-01-24 12:14:06,488] [INFO] Target genome list was writen to GCF_900660505.1_50861_E01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:14:06,499] [INFO] Task started: fastANI
[2024-01-24 12:14:06,499] [INFO] Running command: fastANI --query /var/lib/cwl/stge2e263ff-43b8-490a-84a6-3e2283f40b73/GCF_900660505.1_50861_E01-3_genomic.fna.gz --refList GCF_900660505.1_50861_E01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660505.1_50861_E01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:14:10,072] [INFO] Task succeeded: fastANI
[2024-01-24 12:14:10,078] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:14:10,078] [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_000941075.1	s__Mesomycoplasma dispar	99.9983	360	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	99.26	98.51	0.97	0.95	3	conclusive
GCF_001951355.1	s__Mesomycoplasma ovipneumoniae	80.5571	154	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	97.10	95.23	0.91	0.73	7	-
GCF_000815065.1	s__Mesomycoplasma flocculare	80.5165	171	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	99.48	99.31	0.98	0.96	9	-
GCF_000218525.1	s__Mesomycoplasma ovipneumoniae_A	80.2568	164	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	97.12	95.45	0.91	0.88	8	-
GCF_000008205.1	s__Mesomycoplasma hyopneumoniae	80.1331	171	361	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	98.57	98.32	0.96	0.93	23	-
--------------------------------------------------------------------------------
[2024-01-24 12:14:10,081] [INFO] GTDB search result was written to GCF_900660505.1_50861_E01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 12:14:10,081] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:14:10,084] [INFO] DFAST_QC result json was written to GCF_900660505.1_50861_E01-3_genomic.fna/dqc_result.json
[2024-01-24 12:14:10,084] [INFO] DFAST_QC completed!
[2024-01-24 12:14:10,084] [INFO] Total running time: 0h0m27s