[2024-01-24 12:30:51,916] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:51,918] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:51,918] [INFO] DQC Reference Directory: /var/lib/cwl/stgc19b10ad-eb7b-4b2c-b967-3c3e325eec75/dqc_reference
[2024-01-24 12:30:53,235] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:53,236] [INFO] Task started: Prodigal
[2024-01-24 12:30:53,237] [INFO] Running command: gunzip -c /var/lib/cwl/stgb02a382c-281e-4834-9b71-ab49de76e6d3/GCF_003285065.1_ASM328506v1_genomic.fna.gz | prodigal -d GCF_003285065.1_ASM328506v1_genomic.fna/cds.fna -a GCF_003285065.1_ASM328506v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:54,792] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:54,793] [INFO] Task started: HMMsearch
[2024-01-24 12:30:54,793] [INFO] Running command: hmmsearch --tblout GCF_003285065.1_ASM328506v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgc19b10ad-eb7b-4b2c-b967-3c3e325eec75/dqc_reference/reference_markers.hmm GCF_003285065.1_ASM328506v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:54,963] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:54,965] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb02a382c-281e-4834-9b71-ab49de76e6d3/GCF_003285065.1_ASM328506v1_genomic.fna.gz]
[2024-01-24 12:30:54,979] [INFO] Query marker FASTA was written to GCF_003285065.1_ASM328506v1_genomic.fna/markers.fasta
[2024-01-24 12:30:54,980] [INFO] Task started: Blastn
[2024-01-24 12:30:54,980] [INFO] Running command: blastn -query GCF_003285065.1_ASM328506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc19b10ad-eb7b-4b2c-b967-3c3e325eec75/dqc_reference/reference_markers.fasta -out GCF_003285065.1_ASM328506v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:55,554] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:55,558] [INFO] Selected 12 target genomes.
[2024-01-24 12:30:55,558] [INFO] Target genome list was writen to GCF_003285065.1_ASM328506v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:55,564] [INFO] Task started: fastANI
[2024-01-24 12:30:55,565] [INFO] Running command: fastANI --query /var/lib/cwl/stgb02a382c-281e-4834-9b71-ab49de76e6d3/GCF_003285065.1_ASM328506v1_genomic.fna.gz --refList GCF_003285065.1_ASM328506v1_genomic.fna/target_genomes.txt --output GCF_003285065.1_ASM328506v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:57,820] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:57,820] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgc19b10ad-eb7b-4b2c-b967-3c3e325eec75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:57,821] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgc19b10ad-eb7b-4b2c-b967-3c3e325eec75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:57,826] [INFO] Found 4 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 12:30:57,826] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:57,826] [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	100.0	317	318	95	conclusive
Mycoplasmopsis anatis	strain=NCTC10156	GCA_900660655.1	171279	171279	type	True	99.9508	317	318	95	conclusive
Mycoplasmopsis anatis	strain=1340	GCA_000221305.2	171279	171279	type	True	99.8305	285	318	95	conclusive
Mycoplasmopsis cynos	strain=NCTC10142	GCA_900660545.1	171284	171284	type	True	77.8373	54	318	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:57,828] [INFO] DFAST Taxonomy check result was written to GCF_003285065.1_ASM328506v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:57,829] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:57,829] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:57,829] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgc19b10ad-eb7b-4b2c-b967-3c3e325eec75/dqc_reference/checkm_data
[2024-01-24 12:30:57,830] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:57,842] [INFO] Task started: CheckM
[2024-01-24 12:30:57,842] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003285065.1_ASM328506v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003285065.1_ASM328506v1_genomic.fna/checkm_input GCF_003285065.1_ASM328506v1_genomic.fna/checkm_result
[2024-01-24 12:31:11,025] [INFO] Task succeeded: CheckM
[2024-01-24 12:31:11,026] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:31:11,045] [INFO] ===== Completeness check finished =====
[2024-01-24 12:31:11,046] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:31:11,046] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003285065.1_ASM328506v1_genomic.fna/markers.fasta)
[2024-01-24 12:31:11,047] [INFO] Task started: Blastn
[2024-01-24 12:31:11,047] [INFO] Running command: blastn -query GCF_003285065.1_ASM328506v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgc19b10ad-eb7b-4b2c-b967-3c3e325eec75/dqc_reference/reference_markers_gtdb.fasta -out GCF_003285065.1_ASM328506v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:11,881] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:11,885] [INFO] Selected 13 target genomes.
[2024-01-24 12:31:11,885] [INFO] Target genome list was writen to GCF_003285065.1_ASM328506v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:31:11,900] [INFO] Task started: fastANI
[2024-01-24 12:31:11,901] [INFO] Running command: fastANI --query /var/lib/cwl/stgb02a382c-281e-4834-9b71-ab49de76e6d3/GCF_003285065.1_ASM328506v1_genomic.fna.gz --refList GCF_003285065.1_ASM328506v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003285065.1_ASM328506v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:31:15,124] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:15,135] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:31:15,135] [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_900660655.1	s__Mycoplasmopsis_A anatis	99.9508	318	318	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.97	99.95	1.00	1.00	3	conclusive
GCF_007859615.1	s__Mycoplasmopsis_A anserisalpingitidis	84.2144	238	318	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	97.47	97.47	0.93	0.93	2	-
GCF_007858495.1	s__Mycoplasmopsis_A anserisalpingitidis_A	83.975	237	318	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_000025845.1	s__Mycoplasmopsis_A crocodyli	78.6365	50	318	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_009792315.1	s__Mycoplasmopsis_A sp009792315	78.5775	60	318	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_900660545.1	s__Mycoplasmopsis_A cynos	77.8373	54	318	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.10	98.35	0.95	0.90	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:31:15,137] [INFO] GTDB search result was written to GCF_003285065.1_ASM328506v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:31:15,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:31:15,142] [INFO] DFAST_QC result json was written to GCF_003285065.1_ASM328506v1_genomic.fna/dqc_result.json
[2024-01-24 12:31:15,142] [INFO] DFAST_QC completed!
[2024-01-24 12:31:15,142] [INFO] Total running time: 0h0m23s