[2024-01-24 14:30:30,058] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:30:30,060] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:30:30,060] [INFO] DQC Reference Directory: /var/lib/cwl/stgd1892992-b3a4-4d91-808b-51890938d5bd/dqc_reference
[2024-01-24 14:30:31,387] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:30:31,388] [INFO] Task started: Prodigal
[2024-01-24 14:30:31,388] [INFO] Running command: gunzip -c /var/lib/cwl/stg1e9609d8-04c5-4b02-8f0d-5d10399b81f4/GCF_001886855.1_ASM188685v1_genomic.fna.gz | prodigal -d GCF_001886855.1_ASM188685v1_genomic.fna/cds.fna -a GCF_001886855.1_ASM188685v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:30:34,022] [INFO] Task succeeded: Prodigal
[2024-01-24 14:30:34,022] [INFO] Task started: HMMsearch
[2024-01-24 14:30:34,023] [INFO] Running command: hmmsearch --tblout GCF_001886855.1_ASM188685v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd1892992-b3a4-4d91-808b-51890938d5bd/dqc_reference/reference_markers.hmm GCF_001886855.1_ASM188685v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:30:34,165] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:30:34,167] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg1e9609d8-04c5-4b02-8f0d-5d10399b81f4/GCF_001886855.1_ASM188685v1_genomic.fna.gz]
[2024-01-24 14:30:34,185] [INFO] Query marker FASTA was written to GCF_001886855.1_ASM188685v1_genomic.fna/markers.fasta
[2024-01-24 14:30:34,186] [INFO] Task started: Blastn
[2024-01-24 14:30:34,186] [INFO] Running command: blastn -query GCF_001886855.1_ASM188685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1892992-b3a4-4d91-808b-51890938d5bd/dqc_reference/reference_markers.fasta -out GCF_001886855.1_ASM188685v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:34,676] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:34,679] [INFO] Selected 9 target genomes.
[2024-01-24 14:30:34,680] [INFO] Target genome list was writen to GCF_001886855.1_ASM188685v1_genomic.fna/target_genomes.txt
[2024-01-24 14:30:34,689] [INFO] Task started: fastANI
[2024-01-24 14:30:34,689] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e9609d8-04c5-4b02-8f0d-5d10399b81f4/GCF_001886855.1_ASM188685v1_genomic.fna.gz --refList GCF_001886855.1_ASM188685v1_genomic.fna/target_genomes.txt --output GCF_001886855.1_ASM188685v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:30:41,626] [INFO] Task succeeded: fastANI
[2024-01-24 14:30:41,627] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd1892992-b3a4-4d91-808b-51890938d5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:30:41,627] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd1892992-b3a4-4d91-808b-51890938d5bd/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:30:41,634] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:30:41,634] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:30:41,634] [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 citri	strain=R8-A2	GCA_001886855.1	2133	2133	type	True	100.0	540	545	95	conclusive
Spiroplasma phoeniceum	strain=P40	GCA_003339775.1	47835	47835	type	True	92.9867	389	545	95	below_threshold
Spiroplasma chrysopicola	strain=DF-1	GCA_000400935.1	216933	216933	type	True	78.6902	154	545	95	below_threshold
Spiroplasma syrphidicola	strain=EA-1	GCA_000400955.1	216945	216945	type	True	78.5044	173	545	95	below_threshold
Spiroplasma eriocheiris	strain=DSM 21848	GCA_001029265.1	315358	315358	type	True	78.295	130	545	95	below_threshold
Spiroplasma eriocheiris	strain=CCTCC M 207170	GCA_002028345.1	315358	315358	type	True	78.2322	133	545	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:30:41,636] [INFO] DFAST Taxonomy check result was written to GCF_001886855.1_ASM188685v1_genomic.fna/tc_result.tsv
[2024-01-24 14:30:41,637] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:30:41,637] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:30:41,637] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd1892992-b3a4-4d91-808b-51890938d5bd/dqc_reference/checkm_data
[2024-01-24 14:30:41,638] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:30:41,657] [INFO] Task started: CheckM
[2024-01-24 14:30:41,657] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001886855.1_ASM188685v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001886855.1_ASM188685v1_genomic.fna/checkm_input GCF_001886855.1_ASM188685v1_genomic.fna/checkm_result
[2024-01-24 14:30:56,812] [INFO] Task succeeded: CheckM
[2024-01-24 14:30:56,814] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:30:56,832] [INFO] ===== Completeness check finished =====
[2024-01-24 14:30:56,833] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:30:56,833] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001886855.1_ASM188685v1_genomic.fna/markers.fasta)
[2024-01-24 14:30:56,834] [INFO] Task started: Blastn
[2024-01-24 14:30:56,834] [INFO] Running command: blastn -query GCF_001886855.1_ASM188685v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd1892992-b3a4-4d91-808b-51890938d5bd/dqc_reference/reference_markers_gtdb.fasta -out GCF_001886855.1_ASM188685v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:30:57,305] [INFO] Task succeeded: Blastn
[2024-01-24 14:30:57,309] [INFO] Selected 6 target genomes.
[2024-01-24 14:30:57,309] [INFO] Target genome list was writen to GCF_001886855.1_ASM188685v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:30:57,314] [INFO] Task started: fastANI
[2024-01-24 14:30:57,315] [INFO] Running command: fastANI --query /var/lib/cwl/stg1e9609d8-04c5-4b02-8f0d-5d10399b81f4/GCF_001886855.1_ASM188685v1_genomic.fna.gz --refList GCF_001886855.1_ASM188685v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001886855.1_ASM188685v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:31:05,007] [INFO] Task succeeded: fastANI
[2024-01-24 14:31:05,014] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:31:05,014] [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_001886855.1	s__Spiroplasma citri	100.0	540	545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	96.5649	99.60	97.56	0.93	0.87	9	conclusive
GCF_005222125.1	s__Spiroplasma melliferum	96.3975	356	545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	96.5649	99.84	99.69	0.99	0.98	4	-
GCF_003339775.1	s__Spiroplasma phoeniceum	92.9871	392	545	d__Bacteria;p__Firmicutes;c__Bacilli;o__Mycoplasmatales;f__Mycoplasmataceae;g__Spiroplasma	95.0	95.58	95.16	0.84	0.77	4	-
GCF_009866525.1	s__Spiroplasma poulsonii	83.8012	317	545	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	83.0333	269	545	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 14:31:05,016] [INFO] GTDB search result was written to GCF_001886855.1_ASM188685v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:31:05,017] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:31:05,020] [INFO] DFAST_QC result json was written to GCF_001886855.1_ASM188685v1_genomic.fna/dqc_result.json
[2024-01-24 14:31:05,020] [INFO] DFAST_QC completed!
[2024-01-24 14:31:05,021] [INFO] Total running time: 0h0m35s