[2024-01-24 13:49:40,132] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:49:40,134] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:49:40,134] [INFO] DQC Reference Directory: /var/lib/cwl/stg5c5db1e1-c95c-4986-8c1e-88d63b6040fa/dqc_reference
[2024-01-24 13:49:41,355] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:41,356] [INFO] Task started: Prodigal
[2024-01-24 13:49:41,356] [INFO] Running command: gunzip -c /var/lib/cwl/stgaa124261-122b-4f95-9cf6-e9125973de1d/GCF_006228185.1_ASM622818v1_genomic.fna.gz | prodigal -d GCF_006228185.1_ASM622818v1_genomic.fna/cds.fna -a GCF_006228185.1_ASM622818v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:42,605] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:42,606] [INFO] Task started: HMMsearch
[2024-01-24 13:49:42,606] [INFO] Running command: hmmsearch --tblout GCF_006228185.1_ASM622818v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5c5db1e1-c95c-4986-8c1e-88d63b6040fa/dqc_reference/reference_markers.hmm GCF_006228185.1_ASM622818v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:42,787] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:42,789] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgaa124261-122b-4f95-9cf6-e9125973de1d/GCF_006228185.1_ASM622818v1_genomic.fna.gz]
[2024-01-24 13:49:42,805] [INFO] Query marker FASTA was written to GCF_006228185.1_ASM622818v1_genomic.fna/markers.fasta
[2024-01-24 13:49:42,806] [INFO] Task started: Blastn
[2024-01-24 13:49:42,806] [INFO] Running command: blastn -query GCF_006228185.1_ASM622818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5db1e1-c95c-4986-8c1e-88d63b6040fa/dqc_reference/reference_markers.fasta -out GCF_006228185.1_ASM622818v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:43,364] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:43,367] [INFO] Selected 14 target genomes.
[2024-01-24 13:49:43,367] [INFO] Target genome list was writen to GCF_006228185.1_ASM622818v1_genomic.fna/target_genomes.txt
[2024-01-24 13:49:43,424] [INFO] Task started: fastANI
[2024-01-24 13:49:43,424] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa124261-122b-4f95-9cf6-e9125973de1d/GCF_006228185.1_ASM622818v1_genomic.fna.gz --refList GCF_006228185.1_ASM622818v1_genomic.fna/target_genomes.txt --output GCF_006228185.1_ASM622818v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:46,840] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:46,840] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5c5db1e1-c95c-4986-8c1e-88d63b6040fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:46,840] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5c5db1e1-c95c-4986-8c1e-88d63b6040fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:46,845] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:46,845] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:46,846] [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
Mycoplasma nasistruthionis	strain=2F1A	GCA_006228185.1	353852	353852	type	True	100.0	267	267	95	conclusive
Mycoplasmopsis glycophila	strain=NCTC10194	GCA_900660605.1	171285	171285	type	True	80.0487	54	267	95	below_threshold
Mycoplasma leonicaptivi	strain=ATCC 49890	GCA_000622205.1	36742	36742	type	True	78.6091	58	267	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:46,847] [INFO] DFAST Taxonomy check result was written to GCF_006228185.1_ASM622818v1_genomic.fna/tc_result.tsv
[2024-01-24 13:49:46,848] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:46,848] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:46,848] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5c5db1e1-c95c-4986-8c1e-88d63b6040fa/dqc_reference/checkm_data
[2024-01-24 13:49:46,849] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:46,860] [INFO] Task started: CheckM
[2024-01-24 13:49:46,861] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006228185.1_ASM622818v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006228185.1_ASM622818v1_genomic.fna/checkm_input GCF_006228185.1_ASM622818v1_genomic.fna/checkm_result
[2024-01-24 13:49:59,848] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:59,850] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:59,869] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:59,869] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:59,870] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006228185.1_ASM622818v1_genomic.fna/markers.fasta)
[2024-01-24 13:49:59,870] [INFO] Task started: Blastn
[2024-01-24 13:49:59,870] [INFO] Running command: blastn -query GCF_006228185.1_ASM622818v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5c5db1e1-c95c-4986-8c1e-88d63b6040fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_006228185.1_ASM622818v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:50:00,551] [INFO] Task succeeded: Blastn
[2024-01-24 13:50:00,555] [INFO] Selected 17 target genomes.
[2024-01-24 13:50:00,555] [INFO] Target genome list was writen to GCF_006228185.1_ASM622818v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:50:00,571] [INFO] Task started: fastANI
[2024-01-24 13:50:00,572] [INFO] Running command: fastANI --query /var/lib/cwl/stgaa124261-122b-4f95-9cf6-e9125973de1d/GCF_006228185.1_ASM622818v1_genomic.fna.gz --refList GCF_006228185.1_ASM622818v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006228185.1_ASM622818v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:50:03,789] [INFO] Task succeeded: fastANI
[2024-01-24 13:50:03,795] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:50:03,795] [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_006228185.1	s__Mycoplasmopsis_A nasistruthionis	100.0	267	267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	97.87	97.87	0.96	0.96	2	conclusive
GCF_900660605.1	s__Mycoplasmopsis_A glycophilum	79.9473	53	267	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_014352955.1	s__Mycoplasmopsis_A sp014352955	79.6359	64	267	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	79.5227	67	267	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_000622205.1	s__Mycoplasmopsis_A leonicaptivi	78.6091	58	267	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 13:50:03,797] [INFO] GTDB search result was written to GCF_006228185.1_ASM622818v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:50:03,797] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:50:03,800] [INFO] DFAST_QC result json was written to GCF_006228185.1_ASM622818v1_genomic.fna/dqc_result.json
[2024-01-24 13:50:03,800] [INFO] DFAST_QC completed!
[2024-01-24 13:50:03,800] [INFO] Total running time: 0h0m24s