[2024-01-24 13:09:34,006] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:34,009] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:34,009] [INFO] DQC Reference Directory: /var/lib/cwl/stg1feab450-738f-4f61-a4f7-27c97dfaa1b4/dqc_reference
[2024-01-24 13:09:35,407] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,408] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,409] [INFO] Running command: gunzip -c /var/lib/cwl/stg44b2da52-d754-4da9-81da-753b7a4da2b7/GCF_900660545.1_50884_C01-3_genomic.fna.gz | prodigal -d GCF_900660545.1_50884_C01-3_genomic.fna/cds.fna -a GCF_900660545.1_50884_C01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:37,030] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:37,031] [INFO] Task started: HMMsearch
[2024-01-24 13:09:37,031] [INFO] Running command: hmmsearch --tblout GCF_900660545.1_50884_C01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1feab450-738f-4f61-a4f7-27c97dfaa1b4/dqc_reference/reference_markers.hmm GCF_900660545.1_50884_C01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:37,184] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:37,185] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg44b2da52-d754-4da9-81da-753b7a4da2b7/GCF_900660545.1_50884_C01-3_genomic.fna.gz]
[2024-01-24 13:09:37,199] [INFO] Query marker FASTA was written to GCF_900660545.1_50884_C01-3_genomic.fna/markers.fasta
[2024-01-24 13:09:37,199] [INFO] Task started: Blastn
[2024-01-24 13:09:37,199] [INFO] Running command: blastn -query GCF_900660545.1_50884_C01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg1feab450-738f-4f61-a4f7-27c97dfaa1b4/dqc_reference/reference_markers.fasta -out GCF_900660545.1_50884_C01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:37,791] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:37,794] [INFO] Selected 17 target genomes.
[2024-01-24 13:09:37,794] [INFO] Target genome list was writen to GCF_900660545.1_50884_C01-3_genomic.fna/target_genomes.txt
[2024-01-24 13:09:37,804] [INFO] Task started: fastANI
[2024-01-24 13:09:37,804] [INFO] Running command: fastANI --query /var/lib/cwl/stg44b2da52-d754-4da9-81da-753b7a4da2b7/GCF_900660545.1_50884_C01-3_genomic.fna.gz --refList GCF_900660545.1_50884_C01-3_genomic.fna/target_genomes.txt --output GCF_900660545.1_50884_C01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:41,821] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:41,821] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1feab450-738f-4f61-a4f7-27c97dfaa1b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:41,822] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1feab450-738f-4f61-a4f7-27c97dfaa1b4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:41,838] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:09:41,838] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:09:41,839] [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 cynos	strain=NCTC10142	GCA_900660545.1	171284	171284	type	True	100.0	353	354	95	conclusive
Mycoplasmopsis cynos	strain=Rosendal	GCA_006546925.1	171284	171284	type	True	99.2643	160	354	95	conclusive
Mycoplasmopsis canis	strain=NCTC10146	GCA_900660585.1	29555	29555	type	True	79.9147	122	354	95	below_threshold
Mycoplasmopsis canis	strain=PG 14	GCA_000258925.1	29555	29555	type	True	79.7398	108	354	95	below_threshold
Mycoplasmopsis edwardii	strain=NCTC10132	GCA_900476105.1	53558	53558	type	True	79.3824	123	354	95	below_threshold
Mycoplasmopsis bovirhinis	strain=NCTC10118	GCA_900660515.1	29553	29553	type	True	78.9546	88	354	95	below_threshold
Mycoplasma leonicaptivi	strain=ATCC 49890	GCA_000622205.1	36742	36742	type	True	78.6107	79	354	95	below_threshold
Mycoplasmopsis gallinacea	strain=NCTC10183	GCA_900660495.1	29556	29556	type	True	78.5982	57	354	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:41,840] [INFO] DFAST Taxonomy check result was written to GCF_900660545.1_50884_C01-3_genomic.fna/tc_result.tsv
[2024-01-24 13:09:41,841] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:41,841] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:41,841] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1feab450-738f-4f61-a4f7-27c97dfaa1b4/dqc_reference/checkm_data
[2024-01-24 13:09:41,843] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:41,871] [INFO] Task started: CheckM
[2024-01-24 13:09:41,871] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660545.1_50884_C01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660545.1_50884_C01-3_genomic.fna/checkm_input GCF_900660545.1_50884_C01-3_genomic.fna/checkm_result
[2024-01-24 13:09:55,032] [INFO] Task succeeded: CheckM
[2024-01-24 13:09:55,034] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:09:55,051] [INFO] ===== Completeness check finished =====
[2024-01-24 13:09:55,052] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:09:55,052] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660545.1_50884_C01-3_genomic.fna/markers.fasta)
[2024-01-24 13:09:55,053] [INFO] Task started: Blastn
[2024-01-24 13:09:55,053] [INFO] Running command: blastn -query GCF_900660545.1_50884_C01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg1feab450-738f-4f61-a4f7-27c97dfaa1b4/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660545.1_50884_C01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:55,858] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:55,862] [INFO] Selected 21 target genomes.
[2024-01-24 13:09:55,862] [INFO] Target genome list was writen to GCF_900660545.1_50884_C01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:09:55,909] [INFO] Task started: fastANI
[2024-01-24 13:09:55,909] [INFO] Running command: fastANI --query /var/lib/cwl/stg44b2da52-d754-4da9-81da-753b7a4da2b7/GCF_900660545.1_50884_C01-3_genomic.fna.gz --refList GCF_900660545.1_50884_C01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660545.1_50884_C01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:00,644] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:00,652] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:10:00,653] [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_900660545.1	s__Mycoplasmopsis_A cynos	100.0	353	354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.10	98.35	0.95	0.90	3	conclusive
GCF_001553195.1	s__Mycoplasmopsis_A canis	80.3099	118	354	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	98.31	97.62	0.97	0.93	8	-
GCF_900476105.1	s__Mycoplasmopsis_A edwardii	79.4247	123	354	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_012220205.1	s__Mycoplasmopsis_A gallinacea_A	79.2109	62	354	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_900660515.1	s__Mycoplasmopsis_A bovirhinis	78.9646	89	354	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	78.5664	80	354	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_000526955.1	s__Mycoplasmopsis_A cricetuli	77.1248	55	354	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 13:10:00,655] [INFO] GTDB search result was written to GCF_900660545.1_50884_C01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:00,655] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:00,659] [INFO] DFAST_QC result json was written to GCF_900660545.1_50884_C01-3_genomic.fna/dqc_result.json
[2024-01-24 13:10:00,659] [INFO] DFAST_QC completed!
[2024-01-24 13:10:00,659] [INFO] Total running time: 0h0m27s