[2024-01-25 18:12:50,516] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:12:50,518] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:12:50,518] [INFO] DQC Reference Directory: /var/lib/cwl/stg733bda4f-1886-4399-a334-5e45fb44e822/dqc_reference
[2024-01-25 18:12:51,626] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:12:51,626] [INFO] Task started: Prodigal
[2024-01-25 18:12:51,627] [INFO] Running command: gunzip -c /var/lib/cwl/stg55abafa0-f9fa-487c-aacc-dca0ce21be72/GCF_009730595.1_ASM973059v1_genomic.fna.gz | prodigal -d GCF_009730595.1_ASM973059v1_genomic.fna/cds.fna -a GCF_009730595.1_ASM973059v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:12:53,371] [INFO] Task succeeded: Prodigal
[2024-01-25 18:12:53,372] [INFO] Task started: HMMsearch
[2024-01-25 18:12:53,372] [INFO] Running command: hmmsearch --tblout GCF_009730595.1_ASM973059v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg733bda4f-1886-4399-a334-5e45fb44e822/dqc_reference/reference_markers.hmm GCF_009730595.1_ASM973059v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:12:53,510] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:12:53,511] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg55abafa0-f9fa-487c-aacc-dca0ce21be72/GCF_009730595.1_ASM973059v1_genomic.fna.gz]
[2024-01-25 18:12:53,527] [INFO] Query marker FASTA was written to GCF_009730595.1_ASM973059v1_genomic.fna/markers.fasta
[2024-01-25 18:12:53,527] [INFO] Task started: Blastn
[2024-01-25 18:12:53,527] [INFO] Running command: blastn -query GCF_009730595.1_ASM973059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg733bda4f-1886-4399-a334-5e45fb44e822/dqc_reference/reference_markers.fasta -out GCF_009730595.1_ASM973059v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:12:54,021] [INFO] Task succeeded: Blastn
[2024-01-25 18:12:54,023] [INFO] Selected 17 target genomes.
[2024-01-25 18:12:54,024] [INFO] Target genome list was writen to GCF_009730595.1_ASM973059v1_genomic.fna/target_genomes.txt
[2024-01-25 18:12:54,041] [INFO] Task started: fastANI
[2024-01-25 18:12:54,041] [INFO] Running command: fastANI --query /var/lib/cwl/stg55abafa0-f9fa-487c-aacc-dca0ce21be72/GCF_009730595.1_ASM973059v1_genomic.fna.gz --refList GCF_009730595.1_ASM973059v1_genomic.fna/target_genomes.txt --output GCF_009730595.1_ASM973059v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:12:58,537] [INFO] Task succeeded: fastANI
[2024-01-25 18:12:58,537] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg733bda4f-1886-4399-a334-5e45fb44e822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:12:58,537] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg733bda4f-1886-4399-a334-5e45fb44e822/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:12:58,545] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:12:58,545] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:12:58,545] [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
Spiroplasma tabanidicola	strain=TAUS-1	GCA_009730595.1	324079	324079	type	True	100.0	428	428	95	conclusive
Spiroplasma gladiatoris	strain=TG-1	GCA_004379335.1	2143	2143	type	True	82.0129	247	428	95	below_threshold
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	79.458	162	428	95	below_threshold
Spiroplasma helicoides	strain=TABS-2	GCA_001715535.1	216938	216938	type	True	78.9609	160	428	95	below_threshold
Spiroplasma chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	78.8582	147	428	95	below_threshold
Spiroplasma clarkii	strain=CN-5	GCA_002163565.1	2139	2139	type	True	78.5914	87	428	95	below_threshold
Spiroplasma clarkii	strain=CN-5	GCA_002795265.1	2139	2139	type	True	78.5106	91	428	95	below_threshold
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	78.2758	142	428	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	78.2699	131	428	95	below_threshold
Spiroplasma turonicum	strain=Tab4c	GCA_001513715.1	216946	216946	type	True	77.5149	116	428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:12:58,546] [INFO] DFAST Taxonomy check result was written to GCF_009730595.1_ASM973059v1_genomic.fna/tc_result.tsv
[2024-01-25 18:12:58,547] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:12:58,547] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:12:58,547] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg733bda4f-1886-4399-a334-5e45fb44e822/dqc_reference/checkm_data
[2024-01-25 18:12:58,548] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:12:58,562] [INFO] Task started: CheckM
[2024-01-25 18:12:58,563] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009730595.1_ASM973059v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009730595.1_ASM973059v1_genomic.fna/checkm_input GCF_009730595.1_ASM973059v1_genomic.fna/checkm_result
[2024-01-25 18:13:10,589] [INFO] Task succeeded: CheckM
[2024-01-25 18:13:10,590] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:13:10,606] [INFO] ===== Completeness check finished =====
[2024-01-25 18:13:10,606] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:13:10,606] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009730595.1_ASM973059v1_genomic.fna/markers.fasta)
[2024-01-25 18:13:10,606] [INFO] Task started: Blastn
[2024-01-25 18:13:10,606] [INFO] Running command: blastn -query GCF_009730595.1_ASM973059v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg733bda4f-1886-4399-a334-5e45fb44e822/dqc_reference/reference_markers_gtdb.fasta -out GCF_009730595.1_ASM973059v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:13:11,273] [INFO] Task succeeded: Blastn
[2024-01-25 18:13:11,276] [INFO] Selected 18 target genomes.
[2024-01-25 18:13:11,276] [INFO] Target genome list was writen to GCF_009730595.1_ASM973059v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:13:11,310] [INFO] Task started: fastANI
[2024-01-25 18:13:11,310] [INFO] Running command: fastANI --query /var/lib/cwl/stg55abafa0-f9fa-487c-aacc-dca0ce21be72/GCF_009730595.1_ASM973059v1_genomic.fna.gz --refList GCF_009730595.1_ASM973059v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009730595.1_ASM973059v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:13:16,288] [INFO] Task succeeded: fastANI
[2024-01-25 18:13:16,297] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:13:16,297] [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_009730595.1	s__Spiroplasma_A tabanidicola	100.0	428	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_004379335.1	s__Spiroplasma_A gladiatoris	82.0232	247	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000565175.1	s__Spiroplasma_A culicicola	79.458	162	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001715535.1	s__Spiroplasma_A helicoides	79.0301	158	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008086545.1	s__Spiroplasma_A chinense	78.8857	146	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010365805.1	s__Spiroplasma_A sp010365805	78.8632	105	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002795265.1	s__Spiroplasma_A clarkii	78.5106	91	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	99.91	99.91	1.00	1.00	2	-
GCF_002813555.1	s__Spiroplasma_A floricola	78.3575	139	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000439435.1	s__Spiroplasma_A taiwanense	78.2416	132	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001281045.1	s__Spiroplasma_A cantharicola	77.8921	139	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001262715.1	s__Spiroplasma_A turonicum	77.4301	118	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002804125.1	s__Mesoplasma entomophilum	77.2909	52	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.01	98.03	0.96	0.92	3	-
GCF_001199495.1	s__Mycoplasma sp001199495	76.6769	59	428	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mycoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:13:16,298] [INFO] GTDB search result was written to GCF_009730595.1_ASM973059v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:13:16,299] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:13:16,301] [INFO] DFAST_QC result json was written to GCF_009730595.1_ASM973059v1_genomic.fna/dqc_result.json
[2024-01-25 18:13:16,302] [INFO] DFAST_QC completed!
[2024-01-25 18:13:16,302] [INFO] Total running time: 0h0m26s