[2024-01-24 12:47:27,980] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:47:27,982] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:47:27,983] [INFO] DQC Reference Directory: /var/lib/cwl/stg94c53b50-9650-4226-a178-10e34addc696/dqc_reference
[2024-01-24 12:47:29,349] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:47:29,350] [INFO] Task started: Prodigal
[2024-01-24 12:47:29,350] [INFO] Running command: gunzip -c /var/lib/cwl/stg15172376-bd99-4eab-9c7b-e7245348782e/GCF_000702705.1_ASM70270v1_genomic.fna.gz | prodigal -d GCF_000702705.1_ASM70270v1_genomic.fna/cds.fna -a GCF_000702705.1_ASM70270v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:47:30,943] [INFO] Task succeeded: Prodigal
[2024-01-24 12:47:30,944] [INFO] Task started: HMMsearch
[2024-01-24 12:47:30,944] [INFO] Running command: hmmsearch --tblout GCF_000702705.1_ASM70270v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg94c53b50-9650-4226-a178-10e34addc696/dqc_reference/reference_markers.hmm GCF_000702705.1_ASM70270v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:47:31,108] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:47:31,109] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg15172376-bd99-4eab-9c7b-e7245348782e/GCF_000702705.1_ASM70270v1_genomic.fna.gz]
[2024-01-24 12:47:31,127] [INFO] Query marker FASTA was written to GCF_000702705.1_ASM70270v1_genomic.fna/markers.fasta
[2024-01-24 12:47:31,127] [INFO] Task started: Blastn
[2024-01-24 12:47:31,127] [INFO] Running command: blastn -query GCF_000702705.1_ASM70270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94c53b50-9650-4226-a178-10e34addc696/dqc_reference/reference_markers.fasta -out GCF_000702705.1_ASM70270v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:31,714] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:31,717] [INFO] Selected 9 target genomes.
[2024-01-24 12:47:31,717] [INFO] Target genome list was writen to GCF_000702705.1_ASM70270v1_genomic.fna/target_genomes.txt
[2024-01-24 12:47:31,722] [INFO] Task started: fastANI
[2024-01-24 12:47:31,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg15172376-bd99-4eab-9c7b-e7245348782e/GCF_000702705.1_ASM70270v1_genomic.fna.gz --refList GCF_000702705.1_ASM70270v1_genomic.fna/target_genomes.txt --output GCF_000702705.1_ASM70270v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:47:34,225] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:34,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg94c53b50-9650-4226-a178-10e34addc696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:47:34,226] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg94c53b50-9650-4226-a178-10e34addc696/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:47:34,232] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:47:34,232] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:47:34,233] [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 simbae	strain=ATCC 49888	GCA_000702705.1	36744	36744	type	True	100.0	277	278	95	conclusive
Mycoplasmopsis californica	strain=ST-6	GCA_000695835.1	2113	2113	type	True	79.1787	96	278	95	below_threshold
Mycoplasmopsis mucosicanis	strain=1642	GCA_006546935.1	458208	458208	type	True	79.161	84	278	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:47:34,234] [INFO] DFAST Taxonomy check result was written to GCF_000702705.1_ASM70270v1_genomic.fna/tc_result.tsv
[2024-01-24 12:47:34,235] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:47:34,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:47:34,236] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg94c53b50-9650-4226-a178-10e34addc696/dqc_reference/checkm_data
[2024-01-24 12:47:34,237] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:47:34,250] [INFO] Task started: CheckM
[2024-01-24 12:47:34,251] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000702705.1_ASM70270v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000702705.1_ASM70270v1_genomic.fna/checkm_input GCF_000702705.1_ASM70270v1_genomic.fna/checkm_result
[2024-01-24 12:47:47,838] [INFO] Task succeeded: CheckM
[2024-01-24 12:47:47,839] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:47:47,880] [INFO] ===== Completeness check finished =====
[2024-01-24 12:47:47,881] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:47:47,881] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000702705.1_ASM70270v1_genomic.fna/markers.fasta)
[2024-01-24 12:47:47,881] [INFO] Task started: Blastn
[2024-01-24 12:47:47,881] [INFO] Running command: blastn -query GCF_000702705.1_ASM70270v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg94c53b50-9650-4226-a178-10e34addc696/dqc_reference/reference_markers_gtdb.fasta -out GCF_000702705.1_ASM70270v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:47:48,568] [INFO] Task succeeded: Blastn
[2024-01-24 12:47:48,571] [INFO] Selected 13 target genomes.
[2024-01-24 12:47:48,571] [INFO] Target genome list was writen to GCF_000702705.1_ASM70270v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:47:48,623] [INFO] Task started: fastANI
[2024-01-24 12:47:48,623] [INFO] Running command: fastANI --query /var/lib/cwl/stg15172376-bd99-4eab-9c7b-e7245348782e/GCF_000702705.1_ASM70270v1_genomic.fna.gz --refList GCF_000702705.1_ASM70270v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000702705.1_ASM70270v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:47:50,499] [INFO] Task succeeded: fastANI
[2024-01-24 12:47:50,504] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:47:50,504] [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_000702705.1	s__Mycoplasmopsis simbae	100.0	277	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900660525.1	s__Mycoplasmopsis bovigenitalium	79.6526	83	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	95.54	95.19	0.89	0.89	3	-
GCF_000695835.1	s__Mycoplasmopsis californica	79.1787	96	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.13	99.12	0.97	0.97	7	-
GCF_006546935.1	s__Mycoplasmopsis mucosicanis	79.161	84	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018913985.1	s__Mycoplasmopsis zalophidermidis	78.6964	77	278	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.19	99.19	0.94	0.94	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:47:50,508] [INFO] GTDB search result was written to GCF_000702705.1_ASM70270v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:47:50,509] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:47:50,511] [INFO] DFAST_QC result json was written to GCF_000702705.1_ASM70270v1_genomic.fna/dqc_result.json
[2024-01-24 12:47:50,512] [INFO] DFAST_QC completed!
[2024-01-24 12:47:50,512] [INFO] Total running time: 0h0m23s