[2024-01-24 14:32:33,890] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:32:33,892] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:32:33,893] [INFO] DQC Reference Directory: /var/lib/cwl/stg23bc4e0b-80ce-40ff-a764-29af48576ede/dqc_reference
[2024-01-24 14:32:35,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:32:35,341] [INFO] Task started: Prodigal
[2024-01-24 14:32:35,341] [INFO] Running command: gunzip -c /var/lib/cwl/stg76c0b69b-6c81-4d50-93bd-38522786ed03/GCF_900660585.1_51342_E01-3_genomic.fna.gz | prodigal -d GCF_900660585.1_51342_E01-3_genomic.fna/cds.fna -a GCF_900660585.1_51342_E01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:32:37,002] [INFO] Task succeeded: Prodigal
[2024-01-24 14:32:37,003] [INFO] Task started: HMMsearch
[2024-01-24 14:32:37,003] [INFO] Running command: hmmsearch --tblout GCF_900660585.1_51342_E01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23bc4e0b-80ce-40ff-a764-29af48576ede/dqc_reference/reference_markers.hmm GCF_900660585.1_51342_E01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:32:37,179] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:32:37,180] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg76c0b69b-6c81-4d50-93bd-38522786ed03/GCF_900660585.1_51342_E01-3_genomic.fna.gz]
[2024-01-24 14:32:37,196] [INFO] Query marker FASTA was written to GCF_900660585.1_51342_E01-3_genomic.fna/markers.fasta
[2024-01-24 14:32:37,196] [INFO] Task started: Blastn
[2024-01-24 14:32:37,197] [INFO] Running command: blastn -query GCF_900660585.1_51342_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg23bc4e0b-80ce-40ff-a764-29af48576ede/dqc_reference/reference_markers.fasta -out GCF_900660585.1_51342_E01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:37,741] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:37,756] [INFO] Selected 10 target genomes.
[2024-01-24 14:32:37,757] [INFO] Target genome list was writen to GCF_900660585.1_51342_E01-3_genomic.fna/target_genomes.txt
[2024-01-24 14:32:37,767] [INFO] Task started: fastANI
[2024-01-24 14:32:37,767] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c0b69b-6c81-4d50-93bd-38522786ed03/GCF_900660585.1_51342_E01-3_genomic.fna.gz --refList GCF_900660585.1_51342_E01-3_genomic.fna/target_genomes.txt --output GCF_900660585.1_51342_E01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:40,025] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:40,026] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23bc4e0b-80ce-40ff-a764-29af48576ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:40,026] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23bc4e0b-80ce-40ff-a764-29af48576ede/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:40,034] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:32:40,034] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:40,034] [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 canis	strain=NCTC10146	GCA_900660585.1	29555	29555	type	True	100.0	324	326	95	conclusive
Mycoplasmopsis canis	strain=PG 14	GCA_001553195.1	29555	29555	type	True	99.9936	295	326	95	conclusive
Mycoplasmopsis canis	strain=PG 14	GCA_000258925.1	29555	29555	type	True	99.6271	278	326	95	conclusive
Mycoplasmopsis edwardii	strain=NCTC10132	GCA_900476105.1	53558	53558	type	True	82.6917	139	326	95	below_threshold
Mycoplasmopsis cynos	strain=NCTC10142	GCA_900660545.1	171284	171284	type	True	80.0497	116	326	95	below_threshold
Mycoplasmopsis gallopavonis	strain=NCTC10186	GCA_900660635.1	76629	76629	type	True	79.4572	60	326	95	below_threshold
Mycoplasmopsis bovirhinis	strain=NCTC10118	GCA_900660515.1	29553	29553	type	True	78.7486	99	326	95	below_threshold
Mycoplasmopsis gallopavonis	strain=WR1	GCA_003583385.1	76629	76629	type	True	78.2718	50	326	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:40,036] [INFO] DFAST Taxonomy check result was written to GCF_900660585.1_51342_E01-3_genomic.fna/tc_result.tsv
[2024-01-24 14:32:40,036] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:40,037] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:40,037] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23bc4e0b-80ce-40ff-a764-29af48576ede/dqc_reference/checkm_data
[2024-01-24 14:32:40,038] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:40,055] [INFO] Task started: CheckM
[2024-01-24 14:32:40,055] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660585.1_51342_E01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660585.1_51342_E01-3_genomic.fna/checkm_input GCF_900660585.1_51342_E01-3_genomic.fna/checkm_result
[2024-01-24 14:32:54,515] [INFO] Task succeeded: CheckM
[2024-01-24 14:32:54,517] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 4.17%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2024-01-24 14:32:54,538] [INFO] ===== Completeness check finished =====
[2024-01-24 14:32:54,539] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:32:54,539] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660585.1_51342_E01-3_genomic.fna/markers.fasta)
[2024-01-24 14:32:54,540] [INFO] Task started: Blastn
[2024-01-24 14:32:54,540] [INFO] Running command: blastn -query GCF_900660585.1_51342_E01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg23bc4e0b-80ce-40ff-a764-29af48576ede/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660585.1_51342_E01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:32:55,034] [INFO] Task succeeded: Blastn
[2024-01-24 14:32:55,037] [INFO] Selected 14 target genomes.
[2024-01-24 14:32:55,038] [INFO] Target genome list was writen to GCF_900660585.1_51342_E01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:32:55,046] [INFO] Task started: fastANI
[2024-01-24 14:32:55,047] [INFO] Running command: fastANI --query /var/lib/cwl/stg76c0b69b-6c81-4d50-93bd-38522786ed03/GCF_900660585.1_51342_E01-3_genomic.fna.gz --refList GCF_900660585.1_51342_E01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660585.1_51342_E01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:32:57,738] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:57,744] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:32:57,745] [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_001553195.1	s__Mycoplasmopsis_A canis	99.9826	296	326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	98.31	97.62	0.97	0.93	8	conclusive
GCF_900476105.1	s__Mycoplasmopsis_A edwardii	82.5666	141	326	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	80.0894	115	326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.10	98.35	0.95	0.90	3	-
GCF_900660635.1	s__Mycoplasmopsis_A gallopavonis	79.2998	59	326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.97	99.97	1.00	1.00	2	-
GCF_900660515.1	s__Mycoplasmopsis_A bovirhinis	79.0203	101	326	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	98.45	97.89	0.93	0.90	3	-
GCF_000622205.1	s__Mycoplasmopsis_A leonicaptivi	78.7579	83	326	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_000733865.1	s__Mycoplasmopsis_A buteonis	78.3233	58	326	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 14:32:57,746] [INFO] GTDB search result was written to GCF_900660585.1_51342_E01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 14:32:57,747] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:32:57,750] [INFO] DFAST_QC result json was written to GCF_900660585.1_51342_E01-3_genomic.fna/dqc_result.json
[2024-01-24 14:32:57,750] [INFO] DFAST_QC completed!
[2024-01-24 14:32:57,750] [INFO] Total running time: 0h0m24s