[2024-01-24 15:18:25,776] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:18:25,781] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:18:25,781] [INFO] DQC Reference Directory: /var/lib/cwl/stg55e4cdc8-75de-4715-895f-a52a50f2309d/dqc_reference
[2024-01-24 15:18:27,125] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:18:27,126] [INFO] Task started: Prodigal
[2024-01-24 15:18:27,126] [INFO] Running command: gunzip -c /var/lib/cwl/stg0f90a0e1-84d8-41bd-ae44-59a0bc3a5bbf/GCF_030436345.1_ASM3043634v1_genomic.fna.gz | prodigal -d GCF_030436345.1_ASM3043634v1_genomic.fna/cds.fna -a GCF_030436345.1_ASM3043634v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:18:29,026] [INFO] Task succeeded: Prodigal
[2024-01-24 15:18:29,026] [INFO] Task started: HMMsearch
[2024-01-24 15:18:29,027] [INFO] Running command: hmmsearch --tblout GCF_030436345.1_ASM3043634v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg55e4cdc8-75de-4715-895f-a52a50f2309d/dqc_reference/reference_markers.hmm GCF_030436345.1_ASM3043634v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:18:29,313] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:18:29,315] [INFO] Found 6/6 markers.
[2024-01-24 15:18:29,330] [INFO] Query marker FASTA was written to GCF_030436345.1_ASM3043634v1_genomic.fna/markers.fasta
[2024-01-24 15:18:29,331] [INFO] Task started: Blastn
[2024-01-24 15:18:29,331] [INFO] Running command: blastn -query GCF_030436345.1_ASM3043634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55e4cdc8-75de-4715-895f-a52a50f2309d/dqc_reference/reference_markers.fasta -out GCF_030436345.1_ASM3043634v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:32,844] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:32,848] [INFO] Selected 13 target genomes.
[2024-01-24 15:18:32,849] [INFO] Target genome list was writen to GCF_030436345.1_ASM3043634v1_genomic.fna/target_genomes.txt
[2024-01-24 15:18:32,953] [INFO] Task started: fastANI
[2024-01-24 15:18:32,953] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f90a0e1-84d8-41bd-ae44-59a0bc3a5bbf/GCF_030436345.1_ASM3043634v1_genomic.fna.gz --refList GCF_030436345.1_ASM3043634v1_genomic.fna/target_genomes.txt --output GCF_030436345.1_ASM3043634v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:18:37,353] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:37,354] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg55e4cdc8-75de-4715-895f-a52a50f2309d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:18:37,355] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg55e4cdc8-75de-4715-895f-a52a50f2309d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:18:37,369] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:18:37,369] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:18:37,370] [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
Borreliella valaisiana	strain=VS116	GCA_000170955.2	62088	62088	type	True	94.4651	330	334	95	below_threshold
Borreliella yangtzensis	strain=DSM 24625	GCA_014201775.1	683292	683292	type	True	93.4328	324	334	95	below_threshold
Borreliella garinii subsp. bavariensis	strain=PBi	GCA_000196215.1	664662	29519	type	True	92.6827	321	334	95	below_threshold
Borreliella afzelii	strain=DSM 10508	GCA_014202295.1	29518	29518	type	True	92.6762	326	334	95	below_threshold
Borreliella garinii	strain=20047	GCA_003814405.1	29519	29519	type	True	92.6156	326	334	95	below_threshold
Borreliella garinii	strain=CIP 103362	GCA_001922545.1	29519	29519	type	True	92.5802	327	334	95	below_threshold
Borreliella garinii subsp. bavariensis	strain=PBi	GCA_003814425.1	664662	29519	type	True	92.4922	324	334	95	below_threshold
Borreliella japonica	strain=ATCC 51557	GCA_900099615.1	34095	34095	type	True	92.1835	322	334	95	below_threshold
Borreliella mayonii	strain=MN14-1420	GCA_001945665.1	1674146	1674146	type	True	92.1579	329	334	95	below_threshold
Borreliella lanei	strain=DSM 17992	GCA_014205895.1	373540	373540	type	True	91.9592	323	334	95	below_threshold
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	91.928	327	334	95	below_threshold
Borrelia hermsii	strain=DAH	GCA_023035675.1	140	140	suspected-type	True	78.3647	149	334	95	below_threshold
Borrelia puertoricensis	strain=SUM	GCA_023035875.1	2756107	2756107	type	True	77.9385	158	334	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:18:37,374] [INFO] DFAST Taxonomy check result was written to GCF_030436345.1_ASM3043634v1_genomic.fna/tc_result.tsv
[2024-01-24 15:18:37,374] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:18:37,375] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:18:37,375] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg55e4cdc8-75de-4715-895f-a52a50f2309d/dqc_reference/checkm_data
[2024-01-24 15:18:37,376] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:18:37,393] [INFO] Task started: CheckM
[2024-01-24 15:18:37,394] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030436345.1_ASM3043634v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030436345.1_ASM3043634v1_genomic.fna/checkm_input GCF_030436345.1_ASM3043634v1_genomic.fna/checkm_result
[2024-01-24 15:18:53,360] [INFO] Task succeeded: CheckM
[2024-01-24 15:18:53,361] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:18:53,397] [INFO] ===== Completeness check finished =====
[2024-01-24 15:18:53,397] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:18:53,398] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030436345.1_ASM3043634v1_genomic.fna/markers.fasta)
[2024-01-24 15:18:53,398] [INFO] Task started: Blastn
[2024-01-24 15:18:53,398] [INFO] Running command: blastn -query GCF_030436345.1_ASM3043634v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg55e4cdc8-75de-4715-895f-a52a50f2309d/dqc_reference/reference_markers_gtdb.fasta -out GCF_030436345.1_ASM3043634v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:18:54,544] [INFO] Task succeeded: Blastn
[2024-01-24 15:18:54,547] [INFO] Selected 9 target genomes.
[2024-01-24 15:18:54,547] [INFO] Target genome list was writen to GCF_030436345.1_ASM3043634v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:18:54,553] [INFO] Task started: fastANI
[2024-01-24 15:18:54,554] [INFO] Running command: fastANI --query /var/lib/cwl/stg0f90a0e1-84d8-41bd-ae44-59a0bc3a5bbf/GCF_030436345.1_ASM3043634v1_genomic.fna.gz --refList GCF_030436345.1_ASM3043634v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030436345.1_ASM3043634v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:18:57,588] [INFO] Task succeeded: fastANI
[2024-01-24 15:18:57,597] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:18:57,598] [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_000170955.2	s__Borreliella valaisiana	94.4172	331	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.52	99.04	0.95	0.92	14	-
GCF_014201775.1	s__Borreliella yangtzensis	93.4328	324	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014202295.1	s__Borreliella afzelii	92.6341	327	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.29	99.08	0.96	0.92	10	-
GCF_001922545.1	s__Borreliella garinii	92.5802	327	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	97.97	96.83	0.94	0.85	112	-
GCF_900099615.1	s__Borreliella japonica	92.1835	322	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001945665.1	s__Borreliella mayonii	92.1579	329	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	100.00	100.00	1.00	1.00	2	-
GCF_008828755.2	s__Borreliella turdi	92.1023	324	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	99.10	99.04	0.96	0.96	3	-
GCF_014205895.1	s__Borreliella lanei	91.9592	323	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014205885.1	s__Borreliella californiensis	91.789	326	334	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borreliella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:18:57,602] [INFO] GTDB search result was written to GCF_030436345.1_ASM3043634v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:18:57,603] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:18:57,609] [INFO] DFAST_QC result json was written to GCF_030436345.1_ASM3043634v1_genomic.fna/dqc_result.json
[2024-01-24 15:18:57,609] [INFO] DFAST_QC completed!
[2024-01-24 15:18:57,609] [INFO] Total running time: 0h0m32s