[2024-01-24 14:06:00,164] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:00,165] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:00,166] [INFO] DQC Reference Directory: /var/lib/cwl/stgb75e55e4-2f92-4773-af3d-cfe272c6561e/dqc_reference
[2024-01-24 14:06:01,413] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:06:01,414] [INFO] Task started: Prodigal
[2024-01-24 14:06:01,414] [INFO] Running command: gunzip -c /var/lib/cwl/stg5467abbb-b496-448d-ad47-f7f48c8ac291/GCF_003339775.1_ASM333977v1_genomic.fna.gz | prodigal -d GCF_003339775.1_ASM333977v1_genomic.fna/cds.fna -a GCF_003339775.1_ASM333977v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:06:04,338] [INFO] Task succeeded: Prodigal
[2024-01-24 14:06:04,339] [INFO] Task started: HMMsearch
[2024-01-24 14:06:04,339] [INFO] Running command: hmmsearch --tblout GCF_003339775.1_ASM333977v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb75e55e4-2f92-4773-af3d-cfe272c6561e/dqc_reference/reference_markers.hmm GCF_003339775.1_ASM333977v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:06:04,533] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:06:04,534] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg5467abbb-b496-448d-ad47-f7f48c8ac291/GCF_003339775.1_ASM333977v1_genomic.fna.gz]
[2024-01-24 14:06:04,561] [INFO] Query marker FASTA was written to GCF_003339775.1_ASM333977v1_genomic.fna/markers.fasta
[2024-01-24 14:06:04,562] [INFO] Task started: Blastn
[2024-01-24 14:06:04,562] [INFO] Running command: blastn -query GCF_003339775.1_ASM333977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb75e55e4-2f92-4773-af3d-cfe272c6561e/dqc_reference/reference_markers.fasta -out GCF_003339775.1_ASM333977v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:05,060] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:05,064] [INFO] Selected 12 target genomes.
[2024-01-24 14:06:05,065] [INFO] Target genome list was writen to GCF_003339775.1_ASM333977v1_genomic.fna/target_genomes.txt
[2024-01-24 14:06:05,092] [INFO] Task started: fastANI
[2024-01-24 14:06:05,092] [INFO] Running command: fastANI --query /var/lib/cwl/stg5467abbb-b496-448d-ad47-f7f48c8ac291/GCF_003339775.1_ASM333977v1_genomic.fna.gz --refList GCF_003339775.1_ASM333977v1_genomic.fna/target_genomes.txt --output GCF_003339775.1_ASM333977v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:06:13,068] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:13,068] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb75e55e4-2f92-4773-af3d-cfe272c6561e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:06:13,069] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb75e55e4-2f92-4773-af3d-cfe272c6561e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:06:13,081] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:06:13,081] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:06:13,081] [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 phoeniceum	strain=P40	GCA_003339775.1	47835	47835	type	True	100.0	619	634	95	conclusive
Spiroplasma citri	strain=R8-A2	GCA_001886855.1	2133	2133	type	True	92.8762	393	634	95	below_threshold
Spiroplasma mirum	strain=ATCC 29335	GCA_000517365.1	2144	2144	suspected-type	True	78.5748	151	634	95	below_threshold
Spiroplasma chrysopicola	strain=DF-1	GCA_000400935.1	216933	216933	type	True	78.5055	158	634	95	below_threshold
Spiroplasma syrphidicola	strain=EA-1	GCA_000400955.1	216945	216945	type	True	78.3737	170	634	95	below_threshold
Spiroplasma eriocheiris	strain=DSM 21848	GCA_001029265.1	315358	315358	type	True	78.2106	138	634	95	below_threshold
Spiroplasma eriocheiris	strain=CCTCC M 207170	GCA_002028345.1	315358	315358	type	True	78.1866	136	634	95	below_threshold
Mycoplasma feriruminatoris	strain=G5847	GCA_000327395.2	1179777	1179777	type	True	75.9168	51	634	95	below_threshold
Mycoplasma leachii	strain=PG50	GCA_000183365.1	2105	2105	type	True	75.6238	60	634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:06:13,083] [INFO] DFAST Taxonomy check result was written to GCF_003339775.1_ASM333977v1_genomic.fna/tc_result.tsv
[2024-01-24 14:06:13,084] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:06:13,084] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:06:13,084] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb75e55e4-2f92-4773-af3d-cfe272c6561e/dqc_reference/checkm_data
[2024-01-24 14:06:13,086] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:06:13,112] [INFO] Task started: CheckM
[2024-01-24 14:06:13,112] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003339775.1_ASM333977v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003339775.1_ASM333977v1_genomic.fna/checkm_input GCF_003339775.1_ASM333977v1_genomic.fna/checkm_result
[2024-01-24 14:06:30,409] [INFO] Task succeeded: CheckM
[2024-01-24 14:06:30,410] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:06:30,434] [INFO] ===== Completeness check finished =====
[2024-01-24 14:06:30,434] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:06:30,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003339775.1_ASM333977v1_genomic.fna/markers.fasta)
[2024-01-24 14:06:30,435] [INFO] Task started: Blastn
[2024-01-24 14:06:30,436] [INFO] Running command: blastn -query GCF_003339775.1_ASM333977v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb75e55e4-2f92-4773-af3d-cfe272c6561e/dqc_reference/reference_markers_gtdb.fasta -out GCF_003339775.1_ASM333977v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:06:30,930] [INFO] Task succeeded: Blastn
[2024-01-24 14:06:30,933] [INFO] Selected 6 target genomes.
[2024-01-24 14:06:30,933] [INFO] Target genome list was writen to GCF_003339775.1_ASM333977v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:06:30,938] [INFO] Task started: fastANI
[2024-01-24 14:06:30,939] [INFO] Running command: fastANI --query /var/lib/cwl/stg5467abbb-b496-448d-ad47-f7f48c8ac291/GCF_003339775.1_ASM333977v1_genomic.fna.gz --refList GCF_003339775.1_ASM333977v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003339775.1_ASM333977v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:06:39,579] [INFO] Task succeeded: fastANI
[2024-01-24 14:06:39,589] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:06:39,589] [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_003339775.1	s__Spiroplasma phoeniceum	100.0	623	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	95.0	95.58	95.16	0.84	0.77	4	conclusive
GCF_001886855.1	s__Spiroplasma citri	92.9042	397	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	96.5649	99.60	97.56	0.93	0.87	9	-
GCF_005222125.1	s__Spiroplasma melliferum	91.406	358	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	96.5649	99.84	99.69	0.99	0.98	4	-
GCF_009866525.1	s__Spiroplasma poulsonii	83.6831	350	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	95.0	99.38	98.03	0.90	0.75	6	-
GCF_001886495.1	s__Spiroplasma sp001886495	82.9178	265	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001029265.1	s__Spiroplasma eriocheiris	78.2857	137	634	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:06:39,591] [INFO] GTDB search result was written to GCF_003339775.1_ASM333977v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:06:39,591] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:06:39,597] [INFO] DFAST_QC result json was written to GCF_003339775.1_ASM333977v1_genomic.fna/dqc_result.json
[2024-01-24 14:06:39,597] [INFO] DFAST_QC completed!
[2024-01-24 14:06:39,597] [INFO] Total running time: 0h0m39s