[2024-01-24 14:39:15,523] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,525] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,525] [INFO] DQC Reference Directory: /var/lib/cwl/stg97c6c279-507c-4195-82b9-be6d69cbd609/dqc_reference
[2024-01-24 14:39:16,712] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,713] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,713] [INFO] Running command: gunzip -c /var/lib/cwl/stgd75eb2ce-44c3-4cd4-a3c3-437100b1b0f4/GCF_001281045.1_ASM128104v1_genomic.fna.gz | prodigal -d GCF_001281045.1_ASM128104v1_genomic.fna/cds.fna -a GCF_001281045.1_ASM128104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:18,584] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:18,584] [INFO] Task started: HMMsearch
[2024-01-24 14:39:18,585] [INFO] Running command: hmmsearch --tblout GCF_001281045.1_ASM128104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg97c6c279-507c-4195-82b9-be6d69cbd609/dqc_reference/reference_markers.hmm GCF_001281045.1_ASM128104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:18,768] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:18,769] [WARNING] Found 5/6 markers. [/var/lib/cwl/stgd75eb2ce-44c3-4cd4-a3c3-437100b1b0f4/GCF_001281045.1_ASM128104v1_genomic.fna.gz]
[2024-01-24 14:39:18,786] [INFO] Query marker FASTA was written to GCF_001281045.1_ASM128104v1_genomic.fna/markers.fasta
[2024-01-24 14:39:18,786] [INFO] Task started: Blastn
[2024-01-24 14:39:18,787] [INFO] Running command: blastn -query GCF_001281045.1_ASM128104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97c6c279-507c-4195-82b9-be6d69cbd609/dqc_reference/reference_markers.fasta -out GCF_001281045.1_ASM128104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:19,429] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:19,433] [INFO] Selected 10 target genomes.
[2024-01-24 14:39:19,433] [INFO] Target genome list was writen to GCF_001281045.1_ASM128104v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:19,443] [INFO] Task started: fastANI
[2024-01-24 14:39:19,443] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75eb2ce-44c3-4cd4-a3c3-437100b1b0f4/GCF_001281045.1_ASM128104v1_genomic.fna.gz --refList GCF_001281045.1_ASM128104v1_genomic.fna/target_genomes.txt --output GCF_001281045.1_ASM128104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:22,626] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:22,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg97c6c279-507c-4195-82b9-be6d69cbd609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:22,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg97c6c279-507c-4195-82b9-be6d69cbd609/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:22,635] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:39:22,635] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:39:22,635] [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 cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	100.0	393	393	95	conclusive
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	82.5477	235	393	95	below_threshold
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	81.801	237	393	95	below_threshold
Spiroplasma monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	81.6707	197	393	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	79.7148	177	393	95	below_threshold
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	79.043	154	393	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:22,637] [INFO] DFAST Taxonomy check result was written to GCF_001281045.1_ASM128104v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:22,638] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:22,638] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:22,638] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg97c6c279-507c-4195-82b9-be6d69cbd609/dqc_reference/checkm_data
[2024-01-24 14:39:22,640] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:22,655] [INFO] Task started: CheckM
[2024-01-24 14:39:22,656] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001281045.1_ASM128104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001281045.1_ASM128104v1_genomic.fna/checkm_input GCF_001281045.1_ASM128104v1_genomic.fna/checkm_result
[2024-01-24 14:39:37,359] [INFO] Task succeeded: CheckM
[2024-01-24 14:39:37,360] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:39:37,378] [INFO] ===== Completeness check finished =====
[2024-01-24 14:39:37,378] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:39:37,379] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001281045.1_ASM128104v1_genomic.fna/markers.fasta)
[2024-01-24 14:39:37,387] [INFO] Task started: Blastn
[2024-01-24 14:39:37,388] [INFO] Running command: blastn -query GCF_001281045.1_ASM128104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg97c6c279-507c-4195-82b9-be6d69cbd609/dqc_reference/reference_markers_gtdb.fasta -out GCF_001281045.1_ASM128104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:38,651] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:38,655] [INFO] Selected 11 target genomes.
[2024-01-24 14:39:38,655] [INFO] Target genome list was writen to GCF_001281045.1_ASM128104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:39:38,692] [INFO] Task started: fastANI
[2024-01-24 14:39:38,693] [INFO] Running command: fastANI --query /var/lib/cwl/stgd75eb2ce-44c3-4cd4-a3c3-437100b1b0f4/GCF_001281045.1_ASM128104v1_genomic.fna.gz --refList GCF_001281045.1_ASM128104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001281045.1_ASM128104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:39:41,403] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:41,411] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:39:41,411] [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_001281045.1	s__Spiroplasma_A cantharicola	100.0	393	393	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_000439455.1	s__Spiroplasma_A diminutum	82.5477	235	393	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	81.9709	209	393	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	81.74	239	393	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_002865545.1	s__Spiroplasma_A monobiae	81.6344	198	393	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	79.685	178	393	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 14:39:41,413] [INFO] GTDB search result was written to GCF_001281045.1_ASM128104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:39:41,413] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:39:41,419] [INFO] DFAST_QC result json was written to GCF_001281045.1_ASM128104v1_genomic.fna/dqc_result.json
[2024-01-24 14:39:41,419] [INFO] DFAST_QC completed!
[2024-01-24 14:39:41,419] [INFO] Total running time: 0h0m26s