[2024-01-25 18:03:35,601] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:03:35,602] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:03:35,602] [INFO] DQC Reference Directory: /var/lib/cwl/stg0af04694-7408-4da5-b18e-1cdd72927860/dqc_reference
[2024-01-25 18:03:36,711] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:03:36,712] [INFO] Task started: Prodigal
[2024-01-25 18:03:36,712] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a946e4f-8742-46f8-bf5e-ce5d260f8546/GCF_000439455.1_ASM43945v1_genomic.fna.gz | prodigal -d GCF_000439455.1_ASM43945v1_genomic.fna/cds.fna -a GCF_000439455.1_ASM43945v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:03:38,048] [INFO] Task succeeded: Prodigal
[2024-01-25 18:03:38,048] [INFO] Task started: HMMsearch
[2024-01-25 18:03:38,048] [INFO] Running command: hmmsearch --tblout GCF_000439455.1_ASM43945v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0af04694-7408-4da5-b18e-1cdd72927860/dqc_reference/reference_markers.hmm GCF_000439455.1_ASM43945v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:03:38,236] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:03:38,237] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3a946e4f-8742-46f8-bf5e-ce5d260f8546/GCF_000439455.1_ASM43945v1_genomic.fna.gz]
[2024-01-25 18:03:38,249] [INFO] Query marker FASTA was written to GCF_000439455.1_ASM43945v1_genomic.fna/markers.fasta
[2024-01-25 18:03:38,249] [INFO] Task started: Blastn
[2024-01-25 18:03:38,249] [INFO] Running command: blastn -query GCF_000439455.1_ASM43945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0af04694-7408-4da5-b18e-1cdd72927860/dqc_reference/reference_markers.fasta -out GCF_000439455.1_ASM43945v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:38,749] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:38,753] [INFO] Selected 12 target genomes.
[2024-01-25 18:03:38,754] [INFO] Target genome list was writen to GCF_000439455.1_ASM43945v1_genomic.fna/target_genomes.txt
[2024-01-25 18:03:38,784] [INFO] Task started: fastANI
[2024-01-25 18:03:38,784] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a946e4f-8742-46f8-bf5e-ce5d260f8546/GCF_000439455.1_ASM43945v1_genomic.fna.gz --refList GCF_000439455.1_ASM43945v1_genomic.fna/target_genomes.txt --output GCF_000439455.1_ASM43945v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:03:42,899] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:42,899] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0af04694-7408-4da5-b18e-1cdd72927860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:03:42,899] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0af04694-7408-4da5-b18e-1cdd72927860/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:03:42,905] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:03:42,905] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:03:42,906] [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 diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	100.0	315	315	95	conclusive
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	83.2197	230	315	95	below_threshold
Spiroplasma monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	82.7898	221	315	95	below_threshold
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	82.4924	232	315	95	below_threshold
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	79.9742	158	315	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	79.8892	175	315	95	below_threshold
Spiroplasma gladiatoris	strain=TG-1	GCA_004379335.1	2143	2143	type	True	78.7774	126	315	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:03:42,907] [INFO] DFAST Taxonomy check result was written to GCF_000439455.1_ASM43945v1_genomic.fna/tc_result.tsv
[2024-01-25 18:03:42,907] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:03:42,908] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:03:42,908] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0af04694-7408-4da5-b18e-1cdd72927860/dqc_reference/checkm_data
[2024-01-25 18:03:42,909] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:03:42,921] [INFO] Task started: CheckM
[2024-01-25 18:03:42,922] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000439455.1_ASM43945v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000439455.1_ASM43945v1_genomic.fna/checkm_input GCF_000439455.1_ASM43945v1_genomic.fna/checkm_result
[2024-01-25 18:03:53,966] [INFO] Task succeeded: CheckM
[2024-01-25 18:03:53,967] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:03:53,980] [INFO] ===== Completeness check finished =====
[2024-01-25 18:03:53,981] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:03:53,981] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000439455.1_ASM43945v1_genomic.fna/markers.fasta)
[2024-01-25 18:03:53,981] [INFO] Task started: Blastn
[2024-01-25 18:03:53,981] [INFO] Running command: blastn -query GCF_000439455.1_ASM43945v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0af04694-7408-4da5-b18e-1cdd72927860/dqc_reference/reference_markers_gtdb.fasta -out GCF_000439455.1_ASM43945v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:03:54,630] [INFO] Task succeeded: Blastn
[2024-01-25 18:03:54,633] [INFO] Selected 8 target genomes.
[2024-01-25 18:03:54,634] [INFO] Target genome list was writen to GCF_000439455.1_ASM43945v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:03:54,643] [INFO] Task started: fastANI
[2024-01-25 18:03:54,643] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a946e4f-8742-46f8-bf5e-ce5d260f8546/GCF_000439455.1_ASM43945v1_genomic.fna.gz --refList GCF_000439455.1_ASM43945v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000439455.1_ASM43945v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:03:56,740] [INFO] Task succeeded: fastANI
[2024-01-25 18:03:56,745] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:03:56,746] [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_000439455.1	s__Spiroplasma_A diminutum	100.0	315	315	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_010365805.1	s__Spiroplasma_A sp010365805	83.4819	226	315	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	83.1817	231	315	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	82.7423	222	315	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	82.4924	232	315	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	79.8892	175	315	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	78.7453	127	315	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:03:56,747] [INFO] GTDB search result was written to GCF_000439455.1_ASM43945v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:03:56,748] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:03:56,754] [INFO] DFAST_QC result json was written to GCF_000439455.1_ASM43945v1_genomic.fna/dqc_result.json
[2024-01-25 18:03:56,754] [INFO] DFAST_QC completed!
[2024-01-25 18:03:56,754] [INFO] Total running time: 0h0m21s