[2024-01-25 19:11:35,556] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:35,557] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:35,557] [INFO] DQC Reference Directory: /var/lib/cwl/stg74857372-2f14-431b-976f-fd90689f7cf9/dqc_reference
[2024-01-25 19:11:36,790] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:36,790] [INFO] Task started: Prodigal
[2024-01-25 19:11:36,791] [INFO] Running command: gunzip -c /var/lib/cwl/stga7c9c61a-4261-4772-88c1-e5196a18caea/GCF_000439435.1_ASM43943v1_genomic.fna.gz | prodigal -d GCF_000439435.1_ASM43943v1_genomic.fna/cds.fna -a GCF_000439435.1_ASM43943v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:38,251] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:38,252] [INFO] Task started: HMMsearch
[2024-01-25 19:11:38,252] [INFO] Running command: hmmsearch --tblout GCF_000439435.1_ASM43943v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg74857372-2f14-431b-976f-fd90689f7cf9/dqc_reference/reference_markers.hmm GCF_000439435.1_ASM43943v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:38,381] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:38,382] [WARNING] Found 4/6 markers. [/var/lib/cwl/stga7c9c61a-4261-4772-88c1-e5196a18caea/GCF_000439435.1_ASM43943v1_genomic.fna.gz]
[2024-01-25 19:11:38,395] [INFO] Query marker FASTA was written to GCF_000439435.1_ASM43943v1_genomic.fna/markers.fasta
[2024-01-25 19:11:38,395] [INFO] Task started: Blastn
[2024-01-25 19:11:38,395] [INFO] Running command: blastn -query GCF_000439435.1_ASM43943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74857372-2f14-431b-976f-fd90689f7cf9/dqc_reference/reference_markers.fasta -out GCF_000439435.1_ASM43943v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:38,892] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:38,894] [INFO] Selected 14 target genomes.
[2024-01-25 19:11:38,895] [INFO] Target genome list was writen to GCF_000439435.1_ASM43943v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:38,903] [INFO] Task started: fastANI
[2024-01-25 19:11:38,903] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c9c61a-4261-4772-88c1-e5196a18caea/GCF_000439435.1_ASM43943v1_genomic.fna.gz --refList GCF_000439435.1_ASM43943v1_genomic.fna/target_genomes.txt --output GCF_000439435.1_ASM43943v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:11:43,224] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:43,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg74857372-2f14-431b-976f-fd90689f7cf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:11:43,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg74857372-2f14-431b-976f-fd90689f7cf9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:11:43,233] [INFO] Found 11 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:11:43,233] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:11:43,233] [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 taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	100.0	361	361	95	conclusive
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	79.8832	169	361	95	below_threshold
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	79.8256	180	361	95	below_threshold
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	79.6444	191	361	95	below_threshold
Spiroplasma monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	78.9756	142	361	95	below_threshold
Spiroplasma culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	78.7547	149	361	95	below_threshold
Spiroplasma litorale	strain=TN-1	GCA_001267155.1	216942	216942	type	True	78.3214	112	361	95	below_threshold
Spiroplasma tabanidicola	strain=TAUS-1	GCA_009730595.1	324079	324079	type	True	78.1224	142	361	95	below_threshold
Mycoplasma feriruminatoris	strain=G5847	GCA_000327395.2	1179777	1179777	type	True	76.9901	61	361	95	below_threshold
Mycoplasma cottewii	strain=VIS	GCA_024918975.1	51364	51364	type	True	76.6455	51	361	95	below_threshold
Mycoplasma mycoides subsp. mycoides	strain=PG1	GCA_000011445.1	2103	2102	type	True	76.4068	71	361	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:11:43,235] [INFO] DFAST Taxonomy check result was written to GCF_000439435.1_ASM43943v1_genomic.fna/tc_result.tsv
[2024-01-25 19:11:43,235] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:11:43,235] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:11:43,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg74857372-2f14-431b-976f-fd90689f7cf9/dqc_reference/checkm_data
[2024-01-25 19:11:43,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:11:43,249] [INFO] Task started: CheckM
[2024-01-25 19:11:43,250] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000439435.1_ASM43943v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000439435.1_ASM43943v1_genomic.fna/checkm_input GCF_000439435.1_ASM43943v1_genomic.fna/checkm_result
[2024-01-25 19:11:54,816] [INFO] Task succeeded: CheckM
[2024-01-25 19:11:54,817] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:11:54,833] [INFO] ===== Completeness check finished =====
[2024-01-25 19:11:54,833] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:11:54,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000439435.1_ASM43943v1_genomic.fna/markers.fasta)
[2024-01-25 19:11:54,834] [INFO] Task started: Blastn
[2024-01-25 19:11:54,834] [INFO] Running command: blastn -query GCF_000439435.1_ASM43943v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg74857372-2f14-431b-976f-fd90689f7cf9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000439435.1_ASM43943v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:55,459] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:55,461] [INFO] Selected 11 target genomes.
[2024-01-25 19:11:55,462] [INFO] Target genome list was writen to GCF_000439435.1_ASM43943v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:11:55,483] [INFO] Task started: fastANI
[2024-01-25 19:11:55,483] [INFO] Running command: fastANI --query /var/lib/cwl/stga7c9c61a-4261-4772-88c1-e5196a18caea/GCF_000439435.1_ASM43943v1_genomic.fna.gz --refList GCF_000439435.1_ASM43943v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000439435.1_ASM43943v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:11:57,774] [INFO] Task succeeded: fastANI
[2024-01-25 19:11:57,780] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:11:57,781] [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_000439435.1	s__Spiroplasma_A taiwanense	100.0	361	361	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	79.8272	180	361	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	79.8209	171	361	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	79.6991	189	361	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	79.0517	151	361	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	78.9142	144	361	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	78.7266	150	361	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_001267155.1	s__Spiroplasma_A litorale	78.2542	114	361	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	78.095	143	361	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 19:11:57,782] [INFO] GTDB search result was written to GCF_000439435.1_ASM43943v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:11:57,783] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:11:57,785] [INFO] DFAST_QC result json was written to GCF_000439435.1_ASM43943v1_genomic.fna/dqc_result.json
[2024-01-25 19:11:57,785] [INFO] DFAST_QC completed!
[2024-01-25 19:11:57,786] [INFO] Total running time: 0h0m22s