[2024-01-25 18:20:20,940] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:20:20,941] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:20:20,942] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf45e224-a757-422a-b4b9-d257bb5171ce/dqc_reference
[2024-01-25 18:20:22,106] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:20:22,107] [INFO] Task started: Prodigal
[2024-01-25 18:20:22,107] [INFO] Running command: gunzip -c /var/lib/cwl/stg07122bc4-05e1-4d11-8f72-d6bca3a04dfe/GCF_028885435.1_ASM2888543v1_genomic.fna.gz | prodigal -d GCF_028885435.1_ASM2888543v1_genomic.fna/cds.fna -a GCF_028885435.1_ASM2888543v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:20:23,717] [INFO] Task succeeded: Prodigal
[2024-01-25 18:20:23,717] [INFO] Task started: HMMsearch
[2024-01-25 18:20:23,717] [INFO] Running command: hmmsearch --tblout GCF_028885435.1_ASM2888543v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf45e224-a757-422a-b4b9-d257bb5171ce/dqc_reference/reference_markers.hmm GCF_028885435.1_ASM2888543v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:20:23,836] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:20:23,837] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg07122bc4-05e1-4d11-8f72-d6bca3a04dfe/GCF_028885435.1_ASM2888543v1_genomic.fna.gz]
[2024-01-25 18:20:23,850] [INFO] Query marker FASTA was written to GCF_028885435.1_ASM2888543v1_genomic.fna/markers.fasta
[2024-01-25 18:20:23,850] [INFO] Task started: Blastn
[2024-01-25 18:20:23,850] [INFO] Running command: blastn -query GCF_028885435.1_ASM2888543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf45e224-a757-422a-b4b9-d257bb5171ce/dqc_reference/reference_markers.fasta -out GCF_028885435.1_ASM2888543v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:24,353] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:24,368] [INFO] Selected 7 target genomes.
[2024-01-25 18:20:24,368] [INFO] Target genome list was writen to GCF_028885435.1_ASM2888543v1_genomic.fna/target_genomes.txt
[2024-01-25 18:20:24,376] [INFO] Task started: fastANI
[2024-01-25 18:20:24,376] [INFO] Running command: fastANI --query /var/lib/cwl/stg07122bc4-05e1-4d11-8f72-d6bca3a04dfe/GCF_028885435.1_ASM2888543v1_genomic.fna.gz --refList GCF_028885435.1_ASM2888543v1_genomic.fna/target_genomes.txt --output GCF_028885435.1_ASM2888543v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:20:27,161] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:27,162] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf45e224-a757-422a-b4b9-d257bb5171ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:20:27,162] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf45e224-a757-422a-b4b9-d257bb5171ce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:20:27,167] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:20:27,167] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:20:27,167] [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
Mesomycoplasma ovipneumoniae	strain=Y98	GCA_001715085.1	29562	29562	suspected-type	True	99.7206	289	360	95	conclusive
Mesomycoplasma ovipneumoniae	strain=ATCC 29419	GCA_001951355.1	29562	29562	suspected-type	True	99.6724	292	360	95	conclusive
Mesomycoplasma dispar	strain=NCTC10125	GCA_900660505.1	86660	86660	type	True	80.4333	162	360	95	below_threshold
Mesomycoplasma dispar	strain=ATCC 27140	GCA_000941075.1	86660	86660	type	True	80.4019	162	360	95	below_threshold
Mesomycoplasma flocculare	strain=Ms42	GCA_000815065.1	2128	2128	type	True	78.9118	129	360	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:20:27,168] [INFO] DFAST Taxonomy check result was written to GCF_028885435.1_ASM2888543v1_genomic.fna/tc_result.tsv
[2024-01-25 18:20:27,169] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:20:27,169] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:20:27,169] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf45e224-a757-422a-b4b9-d257bb5171ce/dqc_reference/checkm_data
[2024-01-25 18:20:27,170] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:20:27,183] [INFO] Task started: CheckM
[2024-01-25 18:20:27,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_028885435.1_ASM2888543v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_028885435.1_ASM2888543v1_genomic.fna/checkm_input GCF_028885435.1_ASM2888543v1_genomic.fna/checkm_result
[2024-01-25 18:20:38,791] [INFO] Task succeeded: CheckM
[2024-01-25 18:20:38,792] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:20:38,810] [INFO] ===== Completeness check finished =====
[2024-01-25 18:20:38,810] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:20:38,811] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_028885435.1_ASM2888543v1_genomic.fna/markers.fasta)
[2024-01-25 18:20:38,811] [INFO] Task started: Blastn
[2024-01-25 18:20:38,811] [INFO] Running command: blastn -query GCF_028885435.1_ASM2888543v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf45e224-a757-422a-b4b9-d257bb5171ce/dqc_reference/reference_markers_gtdb.fasta -out GCF_028885435.1_ASM2888543v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:20:39,488] [INFO] Task succeeded: Blastn
[2024-01-25 18:20:39,491] [INFO] Selected 9 target genomes.
[2024-01-25 18:20:39,491] [INFO] Target genome list was writen to GCF_028885435.1_ASM2888543v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:20:39,499] [INFO] Task started: fastANI
[2024-01-25 18:20:39,499] [INFO] Running command: fastANI --query /var/lib/cwl/stg07122bc4-05e1-4d11-8f72-d6bca3a04dfe/GCF_028885435.1_ASM2888543v1_genomic.fna.gz --refList GCF_028885435.1_ASM2888543v1_genomic.fna/target_genomes_gtdb.txt --output GCF_028885435.1_ASM2888543v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:20:42,747] [INFO] Task succeeded: fastANI
[2024-01-25 18:20:42,752] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:20:42,752] [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_001951355.1	s__Mesomycoplasma ovipneumoniae	99.6724	292	360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	97.10	95.23	0.91	0.73	7	conclusive
GCF_000218525.1	s__Mesomycoplasma ovipneumoniae_A	93.0805	291	360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	97.12	95.45	0.91	0.88	8	-
GCF_000941075.1	s__Mesomycoplasma dispar	80.3893	164	360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	99.26	98.51	0.97	0.95	3	-
GCF_000815065.1	s__Mesomycoplasma flocculare	78.9474	128	360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	99.48	99.31	0.98	0.96	9	-
GCF_015708155.1	s__Mesomycoplasma sp015708155	77.9973	95	360	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Metamycoplasmataceae;g__Mesomycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:20:42,754] [INFO] GTDB search result was written to GCF_028885435.1_ASM2888543v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:20:42,754] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:20:42,756] [INFO] DFAST_QC result json was written to GCF_028885435.1_ASM2888543v1_genomic.fna/dqc_result.json
[2024-01-25 18:20:42,756] [INFO] DFAST_QC completed!
[2024-01-25 18:20:42,756] [INFO] Total running time: 0h0m22s