[2024-01-24 13:48:59,761] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:48:59,763] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:48:59,764] [INFO] DQC Reference Directory: /var/lib/cwl/stg2b89c4b7-0c14-4766-981a-8f4176eca46b/dqc_reference
[2024-01-24 13:49:01,024] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:49:01,024] [INFO] Task started: Prodigal
[2024-01-24 13:49:01,025] [INFO] Running command: gunzip -c /var/lib/cwl/stg0b7a8c67-393f-493a-a0ed-a2b0c8308b93/GCF_900660665.1_57612_D01-3_genomic.fna.gz | prodigal -d GCF_900660665.1_57612_D01-3_genomic.fna/cds.fna -a GCF_900660665.1_57612_D01-3_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:49:02,302] [INFO] Task succeeded: Prodigal
[2024-01-24 13:49:02,303] [INFO] Task started: HMMsearch
[2024-01-24 13:49:02,303] [INFO] Running command: hmmsearch --tblout GCF_900660665.1_57612_D01-3_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2b89c4b7-0c14-4766-981a-8f4176eca46b/dqc_reference/reference_markers.hmm GCF_900660665.1_57612_D01-3_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:49:02,480] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:49:02,482] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg0b7a8c67-393f-493a-a0ed-a2b0c8308b93/GCF_900660665.1_57612_D01-3_genomic.fna.gz]
[2024-01-24 13:49:02,497] [INFO] Query marker FASTA was written to GCF_900660665.1_57612_D01-3_genomic.fna/markers.fasta
[2024-01-24 13:49:02,498] [INFO] Task started: Blastn
[2024-01-24 13:49:02,498] [INFO] Running command: blastn -query GCF_900660665.1_57612_D01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b89c4b7-0c14-4766-981a-8f4176eca46b/dqc_reference/reference_markers.fasta -out GCF_900660665.1_57612_D01-3_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:03,052] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:03,057] [INFO] Selected 17 target genomes.
[2024-01-24 13:49:03,057] [INFO] Target genome list was writen to GCF_900660665.1_57612_D01-3_genomic.fna/target_genomes.txt
[2024-01-24 13:49:03,066] [INFO] Task started: fastANI
[2024-01-24 13:49:03,066] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b7a8c67-393f-493a-a0ed-a2b0c8308b93/GCF_900660665.1_57612_D01-3_genomic.fna.gz --refList GCF_900660665.1_57612_D01-3_genomic.fna/target_genomes.txt --output GCF_900660665.1_57612_D01-3_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:49:07,677] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:07,677] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2b89c4b7-0c14-4766-981a-8f4176eca46b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:49:07,678] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2b89c4b7-0c14-4766-981a-8f4176eca46b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:49:07,684] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:49:07,684] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:49:07,685] [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 maculosa	strain=NCTC10168	GCA_900660665.1	114885	114885	type	True	100.0	306	306	95	conclusive
Mycoplasma tauri	strain=Zaradi2	GCA_016925555.1	547987	547987	type	True	78.8621	66	306	95	below_threshold
Mycoplasmopsis felifaucium	strain=ATCC 43428	GCA_000687775.1	35768	35768	type	True	78.3114	80	306	95	below_threshold
Mycoplasmopsis lipofaciens	strain=ATCC 35015	GCA_000686585.1	114884	114884	type	True	78.2006	76	306	95	below_threshold
Mycoplasmopsis fermentans	strain=PG18	GCA_000209735.1	2115	2115	type	True	78.1814	70	306	95	below_threshold
Mycoplasmopsis primatum	strain=ATCC 25948	GCA_000702785.1	55604	55604	type	True	77.2825	58	306	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:49:07,686] [INFO] DFAST Taxonomy check result was written to GCF_900660665.1_57612_D01-3_genomic.fna/tc_result.tsv
[2024-01-24 13:49:07,686] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:49:07,687] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:49:07,687] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2b89c4b7-0c14-4766-981a-8f4176eca46b/dqc_reference/checkm_data
[2024-01-24 13:49:07,688] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:49:07,703] [INFO] Task started: CheckM
[2024-01-24 13:49:07,703] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900660665.1_57612_D01-3_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900660665.1_57612_D01-3_genomic.fna/checkm_input GCF_900660665.1_57612_D01-3_genomic.fna/checkm_result
[2024-01-24 13:49:20,354] [INFO] Task succeeded: CheckM
[2024-01-24 13:49:20,356] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:49:20,374] [INFO] ===== Completeness check finished =====
[2024-01-24 13:49:20,375] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:49:20,375] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900660665.1_57612_D01-3_genomic.fna/markers.fasta)
[2024-01-24 13:49:20,376] [INFO] Task started: Blastn
[2024-01-24 13:49:20,376] [INFO] Running command: blastn -query GCF_900660665.1_57612_D01-3_genomic.fna/markers.fasta -db /var/lib/cwl/stg2b89c4b7-0c14-4766-981a-8f4176eca46b/dqc_reference/reference_markers_gtdb.fasta -out GCF_900660665.1_57612_D01-3_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:49:21,059] [INFO] Task succeeded: Blastn
[2024-01-24 13:49:21,063] [INFO] Selected 15 target genomes.
[2024-01-24 13:49:21,063] [INFO] Target genome list was writen to GCF_900660665.1_57612_D01-3_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:49:21,074] [INFO] Task started: fastANI
[2024-01-24 13:49:21,074] [INFO] Running command: fastANI --query /var/lib/cwl/stg0b7a8c67-393f-493a-a0ed-a2b0c8308b93/GCF_900660665.1_57612_D01-3_genomic.fna.gz --refList GCF_900660665.1_57612_D01-3_genomic.fna/target_genomes_gtdb.txt --output GCF_900660665.1_57612_D01-3_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:49:24,244] [INFO] Task succeeded: fastANI
[2024-01-24 13:49:24,251] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:49:24,251] [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_900660665.1	s__Mycoplasmopsis maculosa	100.0	306	306	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_016925555.1	s__Mycoplasmopsis sp016925555	78.7953	67	306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000687775.1	s__Mycoplasmopsis felifaucium	78.3114	80	306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000686585.1	s__Mycoplasmopsis lipofaciens	78.1524	77	306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017084445.1	s__Mycoplasmopsis sp017084445	78.016	50	306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000266865.1	s__Mycoplasmopsis agalactiae_A	77.7507	63	306	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mycoplasmopsis	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000702785.1	s__Mycoplasmopsis primatum	77.3282	57	306	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 13:49:24,255] [INFO] GTDB search result was written to GCF_900660665.1_57612_D01-3_genomic.fna/result_gtdb.tsv
[2024-01-24 13:49:24,257] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:49:24,260] [INFO] DFAST_QC result json was written to GCF_900660665.1_57612_D01-3_genomic.fna/dqc_result.json
[2024-01-24 13:49:24,261] [INFO] DFAST_QC completed!
[2024-01-24 13:49:24,261] [INFO] Total running time: 0h0m24s