[2024-01-24 13:25:27,671] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:25:27,674] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:25:27,674] [INFO] DQC Reference Directory: /var/lib/cwl/stgb170d6f3-d19a-4842-9cc2-bb26a338c2e8/dqc_reference
[2024-01-24 13:25:28,954] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:25:28,955] [INFO] Task started: Prodigal
[2024-01-24 13:25:28,955] [INFO] Running command: gunzip -c /var/lib/cwl/stg99abba42-117b-4856-af73-181e7e81e91e/GCF_008086545.1_ASM808654v1_genomic.fna.gz | prodigal -d GCF_008086545.1_ASM808654v1_genomic.fna/cds.fna -a GCF_008086545.1_ASM808654v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:25:31,263] [INFO] Task succeeded: Prodigal
[2024-01-24 13:25:31,263] [INFO] Task started: HMMsearch
[2024-01-24 13:25:31,263] [INFO] Running command: hmmsearch --tblout GCF_008086545.1_ASM808654v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb170d6f3-d19a-4842-9cc2-bb26a338c2e8/dqc_reference/reference_markers.hmm GCF_008086545.1_ASM808654v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:25:31,484] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:25:31,485] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg99abba42-117b-4856-af73-181e7e81e91e/GCF_008086545.1_ASM808654v1_genomic.fna.gz]
[2024-01-24 13:25:31,504] [INFO] Query marker FASTA was written to GCF_008086545.1_ASM808654v1_genomic.fna/markers.fasta
[2024-01-24 13:25:31,504] [INFO] Task started: Blastn
[2024-01-24 13:25:31,504] [INFO] Running command: blastn -query GCF_008086545.1_ASM808654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb170d6f3-d19a-4842-9cc2-bb26a338c2e8/dqc_reference/reference_markers.fasta -out GCF_008086545.1_ASM808654v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:32,087] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:32,091] [INFO] Selected 20 target genomes.
[2024-01-24 13:25:32,092] [INFO] Target genome list was writen to GCF_008086545.1_ASM808654v1_genomic.fna/target_genomes.txt
[2024-01-24 13:25:32,415] [INFO] Task started: fastANI
[2024-01-24 13:25:32,416] [INFO] Running command: fastANI --query /var/lib/cwl/stg99abba42-117b-4856-af73-181e7e81e91e/GCF_008086545.1_ASM808654v1_genomic.fna.gz --refList GCF_008086545.1_ASM808654v1_genomic.fna/target_genomes.txt --output GCF_008086545.1_ASM808654v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:25:37,818] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:37,819] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb170d6f3-d19a-4842-9cc2-bb26a338c2e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:25:37,819] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb170d6f3-d19a-4842-9cc2-bb26a338c2e8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:25:37,835] [INFO] Found 15 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:25:37,835] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:25:37,836] [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 chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	100.0	456	456	95	conclusive
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	80.3287	191	456	95	below_threshold
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	79.3234	141	456	95	below_threshold
Spiroplasma gladiatoris	strain=TG-1	GCA_004379335.1	2143	2143	type	True	79.2103	137	456	95	below_threshold
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	79.1424	121	456	95	below_threshold
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	78.8051	146	456	95	below_threshold
Spiroplasma tabanidicola	strain=TAUS-1	GCA_009730595.1	324079	324079	type	True	78.7078	148	456	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	78.5333	128	456	95	below_threshold
Mycoplasma cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	78.0787	53	456	95	below_threshold
Spiroplasma clarkii	strain=CN-5	GCA_002795265.1	2139	2139	type	True	77.9086	137	456	95	below_threshold
Spiroplasma clarkii	strain=CN-5	GCA_002163565.1	2139	2139	type	True	77.888	135	456	95	below_threshold
Spiroplasma corruscae	strain=EC-1	GCA_002237575.1	216934	216934	type	True	77.5006	76	456	95	below_threshold
Mesoplasma tabanidae	strain=BARC 857	GCA_002804025.1	219745	219745	type	True	77.4971	52	456	95	below_threshold
Entomoplasma melaleucae	strain=M1	GCA_002804105.1	81459	81459	type	True	77.2463	52	456	95	below_threshold
Entomoplasma melaleucae	strain=ATCC 49191	GCA_000685885.1	81459	81459	type	True	76.5536	56	456	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:25:37,837] [INFO] DFAST Taxonomy check result was written to GCF_008086545.1_ASM808654v1_genomic.fna/tc_result.tsv
[2024-01-24 13:25:37,838] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:25:37,838] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:25:37,838] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb170d6f3-d19a-4842-9cc2-bb26a338c2e8/dqc_reference/checkm_data
[2024-01-24 13:25:37,839] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:25:37,854] [INFO] Task started: CheckM
[2024-01-24 13:25:37,855] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008086545.1_ASM808654v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008086545.1_ASM808654v1_genomic.fna/checkm_input GCF_008086545.1_ASM808654v1_genomic.fna/checkm_result
[2024-01-24 13:25:54,394] [INFO] Task succeeded: CheckM
[2024-01-24 13:25:54,396] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:25:54,415] [INFO] ===== Completeness check finished =====
[2024-01-24 13:25:54,416] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:25:54,416] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008086545.1_ASM808654v1_genomic.fna/markers.fasta)
[2024-01-24 13:25:54,417] [INFO] Task started: Blastn
[2024-01-24 13:25:54,417] [INFO] Running command: blastn -query GCF_008086545.1_ASM808654v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb170d6f3-d19a-4842-9cc2-bb26a338c2e8/dqc_reference/reference_markers_gtdb.fasta -out GCF_008086545.1_ASM808654v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:25:55,191] [INFO] Task succeeded: Blastn
[2024-01-24 13:25:55,194] [INFO] Selected 14 target genomes.
[2024-01-24 13:25:55,194] [INFO] Target genome list was writen to GCF_008086545.1_ASM808654v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:25:55,212] [INFO] Task started: fastANI
[2024-01-24 13:25:55,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg99abba42-117b-4856-af73-181e7e81e91e/GCF_008086545.1_ASM808654v1_genomic.fna.gz --refList GCF_008086545.1_ASM808654v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008086545.1_ASM808654v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:25:58,158] [INFO] Task succeeded: fastANI
[2024-01-24 13:25:58,176] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:25:58,176] [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_008086545.1	s__Spiroplasma_A chinense	100.0	456	456	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_000565175.1	s__Spiroplasma_A culicicola	80.3587	190	456	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	80.0137	142	456	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_000439455.1	s__Spiroplasma_A diminutum	79.3582	140	456	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_004379335.1	s__Spiroplasma_A gladiatoris	79.2103	137	456	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	79.1223	122	456	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_002813555.1	s__Spiroplasma_A floricola	78.8343	145	456	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_009730595.1	s__Spiroplasma_A tabanidicola	78.7357	147	456	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	78.5333	128	456	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	77.7966	136	456	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_002237575.1	s__Spiroplasma_A corruscae	77.5006	76	456	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_002804105.1	s__Mesoplasma melaleucae	77.2463	52	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_002804025.1	s__Mesoplasma tabanidae	77.1311	51	456	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:25:58,187] [INFO] GTDB search result was written to GCF_008086545.1_ASM808654v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:25:58,188] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:25:58,196] [INFO] DFAST_QC result json was written to GCF_008086545.1_ASM808654v1_genomic.fna/dqc_result.json
[2024-01-24 13:25:58,196] [INFO] DFAST_QC completed!
[2024-01-24 13:25:58,196] [INFO] Total running time: 0h0m31s