[2024-01-24 12:30:19,032] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:30:19,034] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:30:19,035] [INFO] DQC Reference Directory: /var/lib/cwl/stgb7eb9ed9-ec96-4b76-9995-12848e75a9b1/dqc_reference
[2024-01-24 12:30:20,264] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:30:20,265] [INFO] Task started: Prodigal
[2024-01-24 12:30:20,266] [INFO] Running command: gunzip -c /var/lib/cwl/stgb93a28f3-1bff-4890-906e-de5f6c6aeeab/GCF_002237575.1_ASM223757v1_genomic.fna.gz | prodigal -d GCF_002237575.1_ASM223757v1_genomic.fna/cds.fna -a GCF_002237575.1_ASM223757v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:30:22,084] [INFO] Task succeeded: Prodigal
[2024-01-24 12:30:22,085] [INFO] Task started: HMMsearch
[2024-01-24 12:30:22,085] [INFO] Running command: hmmsearch --tblout GCF_002237575.1_ASM223757v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb7eb9ed9-ec96-4b76-9995-12848e75a9b1/dqc_reference/reference_markers.hmm GCF_002237575.1_ASM223757v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:30:22,260] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:30:22,261] [WARNING] Found 4/6 markers. [/var/lib/cwl/stgb93a28f3-1bff-4890-906e-de5f6c6aeeab/GCF_002237575.1_ASM223757v1_genomic.fna.gz]
[2024-01-24 12:30:22,280] [INFO] Query marker FASTA was written to GCF_002237575.1_ASM223757v1_genomic.fna/markers.fasta
[2024-01-24 12:30:22,281] [INFO] Task started: Blastn
[2024-01-24 12:30:22,281] [INFO] Running command: blastn -query GCF_002237575.1_ASM223757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7eb9ed9-ec96-4b76-9995-12848e75a9b1/dqc_reference/reference_markers.fasta -out GCF_002237575.1_ASM223757v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:22,843] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:22,848] [INFO] Selected 14 target genomes.
[2024-01-24 12:30:22,848] [INFO] Target genome list was writen to GCF_002237575.1_ASM223757v1_genomic.fna/target_genomes.txt
[2024-01-24 12:30:22,859] [INFO] Task started: fastANI
[2024-01-24 12:30:22,859] [INFO] Running command: fastANI --query /var/lib/cwl/stgb93a28f3-1bff-4890-906e-de5f6c6aeeab/GCF_002237575.1_ASM223757v1_genomic.fna.gz --refList GCF_002237575.1_ASM223757v1_genomic.fna/target_genomes.txt --output GCF_002237575.1_ASM223757v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:30:26,581] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:26,582] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb7eb9ed9-ec96-4b76-9995-12848e75a9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:30:26,582] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb7eb9ed9-ec96-4b76-9995-12848e75a9b1/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:30:26,597] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:30:26,598] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:30:26,598] [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 corruscae	strain=EC-1	GCA_002237575.1	216934	216934	type	True	100.0	400	400	95	conclusive
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	78.1278	104	400	95	below_threshold
Spiroplasma monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	78.1135	73	400	95	below_threshold
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	77.8499	90	400	95	below_threshold
Spiroplasma apis	strain=B31	GCA_000500935.1	2137	2137	type	True	77.7064	56	400	95	below_threshold
Spiroplasma tabanidicola	strain=TAUS-1	GCA_009730595.1	324079	324079	type	True	77.6988	100	400	95	below_threshold
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	77.6818	96	400	95	below_threshold
Spiroplasma chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	77.3796	75	400	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:30:26,599] [INFO] DFAST Taxonomy check result was written to GCF_002237575.1_ASM223757v1_genomic.fna/tc_result.tsv
[2024-01-24 12:30:26,600] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:30:26,600] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:30:26,601] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb7eb9ed9-ec96-4b76-9995-12848e75a9b1/dqc_reference/checkm_data
[2024-01-24 12:30:26,602] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:30:26,621] [INFO] Task started: CheckM
[2024-01-24 12:30:26,622] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002237575.1_ASM223757v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002237575.1_ASM223757v1_genomic.fna/checkm_input GCF_002237575.1_ASM223757v1_genomic.fna/checkm_result
[2024-01-24 12:30:40,956] [INFO] Task succeeded: CheckM
[2024-01-24 12:30:40,958] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:30:40,976] [INFO] ===== Completeness check finished =====
[2024-01-24 12:30:40,976] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:30:40,977] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002237575.1_ASM223757v1_genomic.fna/markers.fasta)
[2024-01-24 12:30:40,977] [INFO] Task started: Blastn
[2024-01-24 12:30:40,977] [INFO] Running command: blastn -query GCF_002237575.1_ASM223757v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb7eb9ed9-ec96-4b76-9995-12848e75a9b1/dqc_reference/reference_markers_gtdb.fasta -out GCF_002237575.1_ASM223757v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:30:41,697] [INFO] Task succeeded: Blastn
[2024-01-24 12:30:41,701] [INFO] Selected 17 target genomes.
[2024-01-24 12:30:41,702] [INFO] Target genome list was writen to GCF_002237575.1_ASM223757v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:30:41,718] [INFO] Task started: fastANI
[2024-01-24 12:30:41,719] [INFO] Running command: fastANI --query /var/lib/cwl/stgb93a28f3-1bff-4890-906e-de5f6c6aeeab/GCF_002237575.1_ASM223757v1_genomic.fna.gz --refList GCF_002237575.1_ASM223757v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002237575.1_ASM223757v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:30:45,529] [INFO] Task succeeded: fastANI
[2024-01-24 12:30:45,538] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:30:45,538] [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_002237575.1	s__Spiroplasma_A corruscae	100.0	400	400	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_001262715.1	s__Spiroplasma_A turonicum	79.7209	201	400	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_001267155.1	s__Spiroplasma_A litorale	78.9848	196	400	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	78.1135	73	400	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	77.8151	91	400	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	77.7137	95	400	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_000500935.1	s__Spiroplasma_A apis	77.6495	57	400	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	77.6329	104	400	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	77.5769	100	400	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	77.3631	76	400	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 12:30:45,541] [INFO] GTDB search result was written to GCF_002237575.1_ASM223757v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:30:45,541] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:30:45,544] [INFO] DFAST_QC result json was written to GCF_002237575.1_ASM223757v1_genomic.fna/dqc_result.json
[2024-01-24 12:30:45,544] [INFO] DFAST_QC completed!
[2024-01-24 12:30:45,545] [INFO] Total running time: 0h0m27s