[2024-01-24 14:05:14,418] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:05:14,422] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:05:14,422] [INFO] DQC Reference Directory: /var/lib/cwl/stge215e487-1cde-4cd9-843d-3a1984b6fafe/dqc_reference
[2024-01-24 14:05:15,616] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:05:15,617] [INFO] Task started: Prodigal
[2024-01-24 14:05:15,617] [INFO] Running command: gunzip -c /var/lib/cwl/stg66d8454b-22be-469e-8b4e-6a473da9226b/GCF_002813555.1_ASM281355v1_genomic.fna.gz | prodigal -d GCF_002813555.1_ASM281355v1_genomic.fna/cds.fna -a GCF_002813555.1_ASM281355v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:05:17,489] [INFO] Task succeeded: Prodigal
[2024-01-24 14:05:17,490] [INFO] Task started: HMMsearch
[2024-01-24 14:05:17,490] [INFO] Running command: hmmsearch --tblout GCF_002813555.1_ASM281355v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge215e487-1cde-4cd9-843d-3a1984b6fafe/dqc_reference/reference_markers.hmm GCF_002813555.1_ASM281355v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:05:17,665] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:05:17,667] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg66d8454b-22be-469e-8b4e-6a473da9226b/GCF_002813555.1_ASM281355v1_genomic.fna.gz]
[2024-01-24 14:05:17,684] [INFO] Query marker FASTA was written to GCF_002813555.1_ASM281355v1_genomic.fna/markers.fasta
[2024-01-24 14:05:17,684] [INFO] Task started: Blastn
[2024-01-24 14:05:17,684] [INFO] Running command: blastn -query GCF_002813555.1_ASM281355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge215e487-1cde-4cd9-843d-3a1984b6fafe/dqc_reference/reference_markers.fasta -out GCF_002813555.1_ASM281355v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:18,231] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:18,235] [INFO] Selected 10 target genomes.
[2024-01-24 14:05:18,235] [INFO] Target genome list was writen to GCF_002813555.1_ASM281355v1_genomic.fna/target_genomes.txt
[2024-01-24 14:05:18,290] [INFO] Task started: fastANI
[2024-01-24 14:05:18,290] [INFO] Running command: fastANI --query /var/lib/cwl/stg66d8454b-22be-469e-8b4e-6a473da9226b/GCF_002813555.1_ASM281355v1_genomic.fna.gz --refList GCF_002813555.1_ASM281355v1_genomic.fna/target_genomes.txt --output GCF_002813555.1_ASM281355v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:05:20,976] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:20,977] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge215e487-1cde-4cd9-843d-3a1984b6fafe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:05:20,977] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge215e487-1cde-4cd9-843d-3a1984b6fafe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:05:20,985] [INFO] Found 8 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:05:20,985] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:05:20,985] [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 floricola	strain=23-6	GCA_002813555.1	216937	216937	type	True	100.0	428	428	95	conclusive
Spiroplasma diminutum	strain=CUAS-1	GCA_000439455.1	216936	216936	type	True	82.9444	235	428	95	below_threshold
Spiroplasma monobiae	strain=MQ-1	GCA_002865545.1	2136	2136	type	True	82.5851	218	428	95	below_threshold
Spiroplasma cantharicola	strain=CC-1	GCA_001281045.1	362837	362837	type	True	81.7109	239	428	95	below_threshold
Spiroplasma taiwanense	strain=CT-1	GCA_000439435.1	2145	2145	type	True	79.4942	198	428	95	below_threshold
Spiroplasma chinense	strain=CCH	GCA_008086545.1	216932	216932	type	True	78.7764	146	428	95	below_threshold
Spiroplasma helicoides	strain=TABS-2	GCA_001715535.1	216938	216938	type	True	78.737	117	428	95	below_threshold
Spiroplasma gladiatoris	strain=TG-1	GCA_004379335.1	2143	2143	type	True	78.1932	145	428	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:05:20,987] [INFO] DFAST Taxonomy check result was written to GCF_002813555.1_ASM281355v1_genomic.fna/tc_result.tsv
[2024-01-24 14:05:20,987] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:05:20,988] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:05:20,988] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge215e487-1cde-4cd9-843d-3a1984b6fafe/dqc_reference/checkm_data
[2024-01-24 14:05:20,990] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:05:21,010] [INFO] Task started: CheckM
[2024-01-24 14:05:21,010] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002813555.1_ASM281355v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002813555.1_ASM281355v1_genomic.fna/checkm_input GCF_002813555.1_ASM281355v1_genomic.fna/checkm_result
[2024-01-24 14:05:34,954] [INFO] Task succeeded: CheckM
[2024-01-24 14:05:34,957] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:05:34,978] [INFO] ===== Completeness check finished =====
[2024-01-24 14:05:34,978] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:05:34,979] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002813555.1_ASM281355v1_genomic.fna/markers.fasta)
[2024-01-24 14:05:34,979] [INFO] Task started: Blastn
[2024-01-24 14:05:34,980] [INFO] Running command: blastn -query GCF_002813555.1_ASM281355v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge215e487-1cde-4cd9-843d-3a1984b6fafe/dqc_reference/reference_markers_gtdb.fasta -out GCF_002813555.1_ASM281355v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:05:35,688] [INFO] Task succeeded: Blastn
[2024-01-24 14:05:35,692] [INFO] Selected 9 target genomes.
[2024-01-24 14:05:35,693] [INFO] Target genome list was writen to GCF_002813555.1_ASM281355v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:05:35,729] [INFO] Task started: fastANI
[2024-01-24 14:05:35,730] [INFO] Running command: fastANI --query /var/lib/cwl/stg66d8454b-22be-469e-8b4e-6a473da9226b/GCF_002813555.1_ASM281355v1_genomic.fna.gz --refList GCF_002813555.1_ASM281355v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002813555.1_ASM281355v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:05:38,355] [INFO] Task succeeded: fastANI
[2024-01-24 14:05:38,372] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:05:38,372] [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_002813555.1	s__Spiroplasma_A floricola	100.0	428	428	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	83.1779	230	428	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	82.9083	236	428	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	82.623	217	428	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	81.6796	240	428	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	79.4681	199	428	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	78.7465	147	428	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_001715535.1	s__Spiroplasma_A helicoides	78.737	117	428	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	78.2184	144	428	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 14:05:38,374] [INFO] GTDB search result was written to GCF_002813555.1_ASM281355v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:05:38,375] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:05:38,380] [INFO] DFAST_QC result json was written to GCF_002813555.1_ASM281355v1_genomic.fna/dqc_result.json
[2024-01-24 14:05:38,380] [INFO] DFAST_QC completed!
[2024-01-24 14:05:38,380] [INFO] Total running time: 0h0m24s