[2024-01-24 15:26:53,738] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:53,739] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:53,740] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1454b2a-3901-4c22-a9be-a810b0941b11/dqc_reference
[2024-01-24 15:26:54,993] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:54,994] [INFO] Task started: Prodigal
[2024-01-24 15:26:54,995] [INFO] Running command: gunzip -c /var/lib/cwl/stgd470c512-a159-4fd2-806e-3caab42b18c2/GCF_004365095.1_ASM436509v1_genomic.fna.gz | prodigal -d GCF_004365095.1_ASM436509v1_genomic.fna/cds.fna -a GCF_004365095.1_ASM436509v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:26:56,399] [INFO] Task succeeded: Prodigal
[2024-01-24 15:26:56,400] [INFO] Task started: HMMsearch
[2024-01-24 15:26:56,400] [INFO] Running command: hmmsearch --tblout GCF_004365095.1_ASM436509v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1454b2a-3901-4c22-a9be-a810b0941b11/dqc_reference/reference_markers.hmm GCF_004365095.1_ASM436509v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:26:56,650] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:26:56,651] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgd470c512-a159-4fd2-806e-3caab42b18c2/GCF_004365095.1_ASM436509v1_genomic.fna.gz]
[2024-01-24 15:26:56,664] [INFO] Query marker FASTA was written to GCF_004365095.1_ASM436509v1_genomic.fna/markers.fasta
[2024-01-24 15:26:56,665] [INFO] Task started: Blastn
[2024-01-24 15:26:56,665] [INFO] Running command: blastn -query GCF_004365095.1_ASM436509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1454b2a-3901-4c22-a9be-a810b0941b11/dqc_reference/reference_markers.fasta -out GCF_004365095.1_ASM436509v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:00,511] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:00,515] [INFO] Selected 10 target genomes.
[2024-01-24 15:27:00,515] [INFO] Target genome list was writen to GCF_004365095.1_ASM436509v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:00,524] [INFO] Task started: fastANI
[2024-01-24 15:27:00,524] [INFO] Running command: fastANI --query /var/lib/cwl/stgd470c512-a159-4fd2-806e-3caab42b18c2/GCF_004365095.1_ASM436509v1_genomic.fna.gz --refList GCF_004365095.1_ASM436509v1_genomic.fna/target_genomes.txt --output GCF_004365095.1_ASM436509v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:02,457] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:02,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1454b2a-3901-4c22-a9be-a810b0941b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:02,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1454b2a-3901-4c22-a9be-a810b0941b11/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:02,513] [INFO] Found 3 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:27:02,513] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:27:02,513] [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 mustelae	strain=ATCC 35214	GCA_004365095.1	171289	171289	type	True	100.0	273	274	95	conclusive
Mycoplasmopsis felis	strain=ATCC 23391	GCA_000701865.1	33923	33923	type	True	77.643	79	274	95	below_threshold
Mycoplasma leonicaptivi	strain=ATCC 49890	GCA_000622205.1	36742	36742	type	True	77.4605	62	274	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:02,515] [INFO] DFAST Taxonomy check result was written to GCF_004365095.1_ASM436509v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:02,515] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:02,516] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:02,516] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1454b2a-3901-4c22-a9be-a810b0941b11/dqc_reference/checkm_data
[2024-01-24 15:27:02,521] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:02,532] [INFO] Task started: CheckM
[2024-01-24 15:27:02,533] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_004365095.1_ASM436509v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_004365095.1_ASM436509v1_genomic.fna/checkm_input GCF_004365095.1_ASM436509v1_genomic.fna/checkm_result
[2024-01-24 15:27:19,494] [INFO] Task succeeded: CheckM
[2024-01-24 15:27:19,495] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:27:19,532] [INFO] ===== Completeness check finished =====
[2024-01-24 15:27:19,533] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:27:19,533] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_004365095.1_ASM436509v1_genomic.fna/markers.fasta)
[2024-01-24 15:27:19,535] [INFO] Task started: Blastn
[2024-01-24 15:27:19,535] [INFO] Running command: blastn -query GCF_004365095.1_ASM436509v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1454b2a-3901-4c22-a9be-a810b0941b11/dqc_reference/reference_markers_gtdb.fasta -out GCF_004365095.1_ASM436509v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:20,534] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:20,538] [INFO] Selected 12 target genomes.
[2024-01-24 15:27:20,538] [INFO] Target genome list was writen to GCF_004365095.1_ASM436509v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:27:20,552] [INFO] Task started: fastANI
[2024-01-24 15:27:20,552] [INFO] Running command: fastANI --query /var/lib/cwl/stgd470c512-a159-4fd2-806e-3caab42b18c2/GCF_004365095.1_ASM436509v1_genomic.fna.gz --refList GCF_004365095.1_ASM436509v1_genomic.fna/target_genomes_gtdb.txt --output GCF_004365095.1_ASM436509v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:27:22,485] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:22,497] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:27:22,497] [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_004365095.1	s__Mycoplasmopsis_A mustelae	100.0	273	274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000701865.1	s__Mycoplasmopsis_A felis	77.6543	78	274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	98.42	98.42	0.96	0.96	2	-
GCF_000622205.1	s__Mycoplasmopsis_A leonicaptivi	77.4605	62	274	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_018913965.1	s__Mycoplasmopsis_A sp018913965	76.6612	56	274	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis_A	95.0	99.26	99.22	0.95	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 15:27:22,499] [INFO] GTDB search result was written to GCF_004365095.1_ASM436509v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:27:22,500] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:27:22,502] [INFO] DFAST_QC result json was written to GCF_004365095.1_ASM436509v1_genomic.fna/dqc_result.json
[2024-01-24 15:27:22,502] [INFO] DFAST_QC completed!
[2024-01-24 15:27:22,502] [INFO] Total running time: 0h0m29s