[2024-01-25 20:17:05,815] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:17:05,816] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:17:05,816] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe703896-0e2e-4810-9579-aacb732c223d/dqc_reference
[2024-01-25 20:17:06,945] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:17:06,946] [INFO] Task started: Prodigal
[2024-01-25 20:17:06,946] [INFO] Running command: gunzip -c /var/lib/cwl/stg204c1296-b40b-4793-88b4-0ecab61da5aa/GCF_000565175.1_ASM56517v1_genomic.fna.gz | prodigal -d GCF_000565175.1_ASM56517v1_genomic.fna/cds.fna -a GCF_000565175.1_ASM56517v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:17:08,678] [INFO] Task succeeded: Prodigal
[2024-01-25 20:17:08,679] [INFO] Task started: HMMsearch
[2024-01-25 20:17:08,679] [INFO] Running command: hmmsearch --tblout GCF_000565175.1_ASM56517v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe703896-0e2e-4810-9579-aacb732c223d/dqc_reference/reference_markers.hmm GCF_000565175.1_ASM56517v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:17:08,862] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:17:08,863] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg204c1296-b40b-4793-88b4-0ecab61da5aa/GCF_000565175.1_ASM56517v1_genomic.fna.gz]
[2024-01-25 20:17:08,879] [INFO] Query marker FASTA was written to GCF_000565175.1_ASM56517v1_genomic.fna/markers.fasta
[2024-01-25 20:17:08,879] [INFO] Task started: Blastn
[2024-01-25 20:17:08,879] [INFO] Running command: blastn -query GCF_000565175.1_ASM56517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe703896-0e2e-4810-9579-aacb732c223d/dqc_reference/reference_markers.fasta -out GCF_000565175.1_ASM56517v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:09,440] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:09,444] [INFO] Selected 11 target genomes.
[2024-01-25 20:17:09,445] [INFO] Target genome list was writen to GCF_000565175.1_ASM56517v1_genomic.fna/target_genomes.txt
[2024-01-25 20:17:09,463] [INFO] Task started: fastANI
[2024-01-25 20:17:09,463] [INFO] Running command: fastANI --query /var/lib/cwl/stg204c1296-b40b-4793-88b4-0ecab61da5aa/GCF_000565175.1_ASM56517v1_genomic.fna.gz --refList GCF_000565175.1_ASM56517v1_genomic.fna/target_genomes.txt --output GCF_000565175.1_ASM56517v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:17:11,799] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:11,800] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe703896-0e2e-4810-9579-aacb732c223d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:17:11,800] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe703896-0e2e-4810-9579-aacb732c223d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:17:11,807] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 20:17:11,807] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:17:11,807] [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 culicicola	strain=AES-1	GCA_000565175.1	216935	216935	type	True	100.0	391	391	95	conclusive
Spiroplasma chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	80.447	188	391	95	below_threshold
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	79.6708	162	391	95	below_threshold
Spiroplasma floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	79.1695	162	391	95	below_threshold
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	78.9548	154	391	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	78.6498	152	391	95	below_threshold
Mesoplasma chauliocola	strain=CHPA-2	GCA_002290085.1	216427	216427	type	True	77.4814	58	391	95	below_threshold
Spiroplasma litorale	strain=TN-1	GCA_001267155.1	216942	216942	type	True	77.4542	105	391	95	below_threshold
Mesoplasma chauliocola	strain=ATCC 49578	GCA_000518825.1	216427	216427	type	True	77.4376	59	391	95	below_threshold
Spiroplasma sabaudiense	strain=Ar-1343	GCA_000565215.1	216944	216944	type	True	76.7506	60	391	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:17:11,809] [INFO] DFAST Taxonomy check result was written to GCF_000565175.1_ASM56517v1_genomic.fna/tc_result.tsv
[2024-01-25 20:17:11,809] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:17:11,809] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:17:11,810] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe703896-0e2e-4810-9579-aacb732c223d/dqc_reference/checkm_data
[2024-01-25 20:17:11,810] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:17:11,824] [INFO] Task started: CheckM
[2024-01-25 20:17:11,825] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000565175.1_ASM56517v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000565175.1_ASM56517v1_genomic.fna/checkm_input GCF_000565175.1_ASM56517v1_genomic.fna/checkm_result
[2024-01-25 20:17:24,863] [INFO] Task succeeded: CheckM
[2024-01-25 20:17:24,864] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:17:24,884] [INFO] ===== Completeness check finished =====
[2024-01-25 20:17:24,884] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:17:24,884] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000565175.1_ASM56517v1_genomic.fna/markers.fasta)
[2024-01-25 20:17:24,885] [INFO] Task started: Blastn
[2024-01-25 20:17:24,885] [INFO] Running command: blastn -query GCF_000565175.1_ASM56517v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe703896-0e2e-4810-9579-aacb732c223d/dqc_reference/reference_markers_gtdb.fasta -out GCF_000565175.1_ASM56517v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:17:25,607] [INFO] Task succeeded: Blastn
[2024-01-25 20:17:25,615] [INFO] Selected 10 target genomes.
[2024-01-25 20:17:25,615] [INFO] Target genome list was writen to GCF_000565175.1_ASM56517v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:17:25,633] [INFO] Task started: fastANI
[2024-01-25 20:17:25,633] [INFO] Running command: fastANI --query /var/lib/cwl/stg204c1296-b40b-4793-88b4-0ecab61da5aa/GCF_000565175.1_ASM56517v1_genomic.fna.gz --refList GCF_000565175.1_ASM56517v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000565175.1_ASM56517v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:17:27,879] [INFO] Task succeeded: fastANI
[2024-01-25 20:17:27,888] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:17:27,888] [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_000565175.1	s__Spiroplasma_A culicicola	100.0	391	391	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_008086545.1	s__Spiroplasma_A chinense	80.4449	188	391	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	79.6365	163	391	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	79.5402	149	391	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	79.1717	161	391	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	78.9548	154	391	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	78.677	151	391	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_002290085.1	s__Mesoplasma chauliocola	77.4814	58	391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Mesoplasma	95.0	99.98	99.98	0.99	0.99	2	-
GCF_001267155.1	s__Spiroplasma_A litorale	77.4258	106	391	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_000565215.1	s__Spiroplasma_B sabaudiense	76.7903	59	391	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma_B	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 20:17:27,889] [INFO] GTDB search result was written to GCF_000565175.1_ASM56517v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:17:27,890] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:17:27,892] [INFO] DFAST_QC result json was written to GCF_000565175.1_ASM56517v1_genomic.fna/dqc_result.json
[2024-01-25 20:17:27,892] [INFO] DFAST_QC completed!
[2024-01-25 20:17:27,893] [INFO] Total running time: 0h0m22s