[2024-01-24 10:58:17,097] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:58:17,098] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:58:17,099] [INFO] DQC Reference Directory: /var/lib/cwl/stg8531130a-c4b4-48b7-987d-5709e2e8494f/dqc_reference
[2024-01-24 10:58:18,329] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:58:18,331] [INFO] Task started: Prodigal
[2024-01-24 10:58:18,331] [INFO] Running command: gunzip -c /var/lib/cwl/stg7cd8a865-033d-4023-bcf9-7ba91d92e97b/GCF_002930185.1_entomo04.02_genomic.fna.gz | prodigal -d GCF_002930185.1_entomo04.02_genomic.fna/cds.fna -a GCF_002930185.1_entomo04.02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:58:20,433] [INFO] Task succeeded: Prodigal
[2024-01-24 10:58:20,434] [INFO] Task started: HMMsearch
[2024-01-24 10:58:20,434] [INFO] Running command: hmmsearch --tblout GCF_002930185.1_entomo04.02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8531130a-c4b4-48b7-987d-5709e2e8494f/dqc_reference/reference_markers.hmm GCF_002930185.1_entomo04.02_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:58:20,594] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:58:20,596] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg7cd8a865-033d-4023-bcf9-7ba91d92e97b/GCF_002930185.1_entomo04.02_genomic.fna.gz]
[2024-01-24 10:58:20,615] [INFO] Query marker FASTA was written to GCF_002930185.1_entomo04.02_genomic.fna/markers.fasta
[2024-01-24 10:58:20,615] [INFO] Task started: Blastn
[2024-01-24 10:58:20,615] [INFO] Running command: blastn -query GCF_002930185.1_entomo04.02_genomic.fna/markers.fasta -db /var/lib/cwl/stg8531130a-c4b4-48b7-987d-5709e2e8494f/dqc_reference/reference_markers.fasta -out GCF_002930185.1_entomo04.02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:21,115] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:21,119] [INFO] Selected 15 target genomes.
[2024-01-24 10:58:21,119] [INFO] Target genome list was writen to GCF_002930185.1_entomo04.02_genomic.fna/target_genomes.txt
[2024-01-24 10:58:21,127] [INFO] Task started: fastANI
[2024-01-24 10:58:21,127] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd8a865-033d-4023-bcf9-7ba91d92e97b/GCF_002930185.1_entomo04.02_genomic.fna.gz --refList GCF_002930185.1_entomo04.02_genomic.fna/target_genomes.txt --output GCF_002930185.1_entomo04.02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:58:26,155] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:26,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8531130a-c4b4-48b7-987d-5709e2e8494f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:58:26,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8531130a-c4b4-48b7-987d-5709e2e8494f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:58:26,164] [INFO] Found 6 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:58:26,164] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:58:26,164] [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
Williamsoniiplasma lucivorax	strain=PIPN-2	GCA_002930185.1	209274	209274	type	True	100.0	372	372	95	conclusive
Williamsoniiplasma lucivorax	strain=ATCC 49196	GCA_000518285.1	209274	209274	type	True	99.9503	350	372	95	conclusive
Williamsoniiplasma luminosum	strain=ATCC 49195	GCA_000526855.1	214888	214888	type	True	80.8155	203	372	95	below_threshold
Williamsoniiplasma luminosum	strain=PIMN-1	GCA_002803985.1	214888	214888	type	True	80.7583	207	372	95	below_threshold
Mesoplasma seiffertii	strain=ATCC 49495	GCA_000518725.1	28224	28224	type	True	78.227	65	372	95	below_threshold
Mesoplasma florum	strain=L1; ATCC 33453	GCA_000008305.1	2151	2151	type	True	77.7151	56	372	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:58:26,166] [INFO] DFAST Taxonomy check result was written to GCF_002930185.1_entomo04.02_genomic.fna/tc_result.tsv
[2024-01-24 10:58:26,167] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:58:26,167] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:58:26,167] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8531130a-c4b4-48b7-987d-5709e2e8494f/dqc_reference/checkm_data
[2024-01-24 10:58:26,168] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:58:26,182] [INFO] Task started: CheckM
[2024-01-24 10:58:26,183] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002930185.1_entomo04.02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002930185.1_entomo04.02_genomic.fna/checkm_input GCF_002930185.1_entomo04.02_genomic.fna/checkm_result
[2024-01-24 10:58:41,086] [INFO] Task succeeded: CheckM
[2024-01-24 10:58:41,088] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:58:41,109] [INFO] ===== Completeness check finished =====
[2024-01-24 10:58:41,110] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:58:41,110] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002930185.1_entomo04.02_genomic.fna/markers.fasta)
[2024-01-24 10:58:41,111] [INFO] Task started: Blastn
[2024-01-24 10:58:41,111] [INFO] Running command: blastn -query GCF_002930185.1_entomo04.02_genomic.fna/markers.fasta -db /var/lib/cwl/stg8531130a-c4b4-48b7-987d-5709e2e8494f/dqc_reference/reference_markers_gtdb.fasta -out GCF_002930185.1_entomo04.02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:58:41,589] [INFO] Task succeeded: Blastn
[2024-01-24 10:58:41,592] [INFO] Selected 18 target genomes.
[2024-01-24 10:58:41,592] [INFO] Target genome list was writen to GCF_002930185.1_entomo04.02_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:58:41,613] [INFO] Task started: fastANI
[2024-01-24 10:58:41,613] [INFO] Running command: fastANI --query /var/lib/cwl/stg7cd8a865-033d-4023-bcf9-7ba91d92e97b/GCF_002930185.1_entomo04.02_genomic.fna.gz --refList GCF_002930185.1_entomo04.02_genomic.fna/target_genomes_gtdb.txt --output GCF_002930185.1_entomo04.02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:58:46,157] [INFO] Task succeeded: fastANI
[2024-01-24 10:58:46,167] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:58:46,167] [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_000518285.1	s__Williamsoniiplasma lucivorax	99.9503	350	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_002803985.1	s__Williamsoniiplasma luminosum	80.7484	206	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Williamsoniiplasma	95.0	97.66	95.33	0.92	0.84	3	-
GCF_000518725.1	s__Tullyiplasma seiffertii	78.227	65	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002804245.1	s__Mesoplasma coleopterae	78.0471	58	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	98.88	98.62	0.96	0.96	3	-
GCF_002843565.1	s__Tullyiplasma syrphidae	78.0344	54	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002804125.1	s__Mesoplasma entomophilum	77.8662	57	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.01	98.03	0.96	0.92	3	-
GCF_000701525.1	s__Mesoplasma grammopterae	77.767	54	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.59	97.19	0.95	0.91	3	-
GCF_000702725.1	s__Tullyiplasma photuris	77.7613	64	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Tullyiplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000008305.1	s__Mesoplasma florum	77.7151	56	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.9326	98.30	97.69	0.92	0.91	10	-
GCF_002804025.1	s__Mesoplasma tabanidae	77.3879	64	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000565175.1	s__Spiroplasma_A culicicola	77.0333	53	372	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 10:58:46,170] [INFO] GTDB search result was written to GCF_002930185.1_entomo04.02_genomic.fna/result_gtdb.tsv
[2024-01-24 10:58:46,171] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:58:46,173] [INFO] DFAST_QC result json was written to GCF_002930185.1_entomo04.02_genomic.fna/dqc_result.json
[2024-01-24 10:58:46,173] [INFO] DFAST_QC completed!
[2024-01-24 10:58:46,173] [INFO] Total running time: 0h0m29s