[2024-01-24 13:43:27,017] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:43:27,019] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:43:27,019] [INFO] DQC Reference Directory: /var/lib/cwl/stg09d1a395-5058-4db3-8777-9bea708b98d6/dqc_reference
[2024-01-24 13:43:28,204] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:43:28,205] [INFO] Task started: Prodigal
[2024-01-24 13:43:28,205] [INFO] Running command: gunzip -c /var/lib/cwl/stg6bd68380-fb1b-44a7-aa7f-bb63d7dac860/GCF_004216495.1_ASM421649v1_genomic.fna.gz | prodigal -d GCF_004216495.1_ASM421649v1_genomic.fna/cds.fna -a GCF_004216495.1_ASM421649v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:29,570] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:29,570] [INFO] Task started: HMMsearch
[2024-01-24 13:43:29,570] [INFO] Running command: hmmsearch --tblout GCF_004216495.1_ASM421649v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg09d1a395-5058-4db3-8777-9bea708b98d6/dqc_reference/reference_markers.hmm GCF_004216495.1_ASM421649v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:29,679] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:29,681] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg6bd68380-fb1b-44a7-aa7f-bb63d7dac860/GCF_004216495.1_ASM421649v1_genomic.fna.gz]
[2024-01-24 13:43:29,693] [INFO] Query marker FASTA was written to GCF_004216495.1_ASM421649v1_genomic.fna/markers.fasta
[2024-01-24 13:43:29,693] [INFO] Task started: Blastn
[2024-01-24 13:43:29,693] [INFO] Running command: blastn -query GCF_004216495.1_ASM421649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09d1a395-5058-4db3-8777-9bea708b98d6/dqc_reference/reference_markers.fasta -out GCF_004216495.1_ASM421649v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:30,222] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:30,225] [INFO] Selected 13 target genomes.
[2024-01-24 13:43:30,225] [INFO] Target genome list was writen to GCF_004216495.1_ASM421649v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:30,283] [INFO] Task started: fastANI
[2024-01-24 13:43:30,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bd68380-fb1b-44a7-aa7f-bb63d7dac860/GCF_004216495.1_ASM421649v1_genomic.fna.gz --refList GCF_004216495.1_ASM421649v1_genomic.fna/target_genomes.txt --output GCF_004216495.1_ASM421649v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:33,957] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:33,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg09d1a395-5058-4db3-8777-9bea708b98d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:33,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg09d1a395-5058-4db3-8777-9bea708b98d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:33,966] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:33,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:33,967] [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 phocirhinis	strain=852	GCA_004216495.1	142650	142650	type	True	100.0	288	288	95	conclusive
Mycoplasmopsis bovigenitalium	strain=NCTC10122	GCA_900660525.1	2112	2112	type	True	78.9858	74	288	95	below_threshold
Mycoplasma miroungigenitalium	strain=ES2806-GEN	GCA_013008635.1	754515	754515	type	True	78.5565	80	288	95	below_threshold
Mycoplasmopsis californica	strain=ST-6	GCA_000695835.1	2113	2113	type	True	78.1421	76	288	95	below_threshold
Mycoplasmopsis mucosicanis	strain=1642	GCA_006546935.1	458208	458208	type	True	77.6186	68	288	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:33,968] [INFO] DFAST Taxonomy check result was written to GCF_004216495.1_ASM421649v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:33,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:33,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:33,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg09d1a395-5058-4db3-8777-9bea708b98d6/dqc_reference/checkm_data
[2024-01-24 13:43:33,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:33,981] [INFO] Task started: CheckM
[2024-01-24 13:43:33,981] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004216495.1_ASM421649v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004216495.1_ASM421649v1_genomic.fna/checkm_input GCF_004216495.1_ASM421649v1_genomic.fna/checkm_result
[2024-01-24 13:43:45,717] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:45,718] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:45,735] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:45,735] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:45,735] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004216495.1_ASM421649v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:45,736] [INFO] Task started: Blastn
[2024-01-24 13:43:45,736] [INFO] Running command: blastn -query GCF_004216495.1_ASM421649v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg09d1a395-5058-4db3-8777-9bea708b98d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_004216495.1_ASM421649v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:46,428] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:46,431] [INFO] Selected 12 target genomes.
[2024-01-24 13:43:46,431] [INFO] Target genome list was writen to GCF_004216495.1_ASM421649v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:46,438] [INFO] Task started: fastANI
[2024-01-24 13:43:46,438] [INFO] Running command: fastANI --query /var/lib/cwl/stg6bd68380-fb1b-44a7-aa7f-bb63d7dac860/GCF_004216495.1_ASM421649v1_genomic.fna.gz --refList GCF_004216495.1_ASM421649v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004216495.1_ASM421649v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:50,028] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:50,034] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:50,034] [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_004216495.1	s__Mycoplasmopsis phocirhinis	100.0	288	288	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	78.9858	74	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	95.54	95.19	0.89	0.89	3	-
GCF_013008635.1	s__Mycoplasmopsis sp013008635	78.609	79	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.85	99.85	1.00	1.00	3	-
GCF_000695835.1	s__Mycoplasmopsis californica	78.1421	76	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.13	99.12	0.97	0.97	7	-
GCF_018913985.1	s__Mycoplasmopsis zalophidermidis	77.8406	85	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	99.19	99.19	0.94	0.94	2	-
GCF_006546935.1	s__Mycoplasmopsis mucosicanis	77.5747	69	288	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:50,036] [INFO] GTDB search result was written to GCF_004216495.1_ASM421649v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:50,036] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:50,039] [INFO] DFAST_QC result json was written to GCF_004216495.1_ASM421649v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:50,039] [INFO] DFAST_QC completed!
[2024-01-24 13:43:50,039] [INFO] Total running time: 0h0m23s