[2024-01-24 11:44:23,630] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:44:23,635] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:44:23,636] [INFO] DQC Reference Directory: /var/lib/cwl/stgac277171-bfdf-4c79-8676-0208c5937951/dqc_reference
[2024-01-24 11:44:26,340] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:44:26,341] [INFO] Task started: Prodigal
[2024-01-24 11:44:26,342] [INFO] Running command: gunzip -c /var/lib/cwl/stg14800fda-08b1-4e6f-b330-62390b988b0d/GCF_003606285.1_ASM360628v1_genomic.fna.gz | prodigal -d GCF_003606285.1_ASM360628v1_genomic.fna/cds.fna -a GCF_003606285.1_ASM360628v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:44:28,585] [INFO] Task succeeded: Prodigal
[2024-01-24 11:44:28,585] [INFO] Task started: HMMsearch
[2024-01-24 11:44:28,585] [INFO] Running command: hmmsearch --tblout GCF_003606285.1_ASM360628v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgac277171-bfdf-4c79-8676-0208c5937951/dqc_reference/reference_markers.hmm GCF_003606285.1_ASM360628v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:44:28,946] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:44:28,948] [INFO] Found 6/6 markers.
[2024-01-24 11:44:28,965] [INFO] Query marker FASTA was written to GCF_003606285.1_ASM360628v1_genomic.fna/markers.fasta
[2024-01-24 11:44:28,966] [INFO] Task started: Blastn
[2024-01-24 11:44:28,966] [INFO] Running command: blastn -query GCF_003606285.1_ASM360628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac277171-bfdf-4c79-8676-0208c5937951/dqc_reference/reference_markers.fasta -out GCF_003606285.1_ASM360628v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:31,458] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:31,461] [INFO] Selected 13 target genomes.
[2024-01-24 11:44:31,461] [INFO] Target genome list was writen to GCF_003606285.1_ASM360628v1_genomic.fna/target_genomes.txt
[2024-01-24 11:44:31,506] [INFO] Task started: fastANI
[2024-01-24 11:44:31,506] [INFO] Running command: fastANI --query /var/lib/cwl/stg14800fda-08b1-4e6f-b330-62390b988b0d/GCF_003606285.1_ASM360628v1_genomic.fna.gz --refList GCF_003606285.1_ASM360628v1_genomic.fna/target_genomes.txt --output GCF_003606285.1_ASM360628v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:44:35,421] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:35,422] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgac277171-bfdf-4c79-8676-0208c5937951/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:44:35,422] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgac277171-bfdf-4c79-8676-0208c5937951/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:44:35,432] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:44:35,433] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:44:35,433] [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
Borrelia turcica	strain=IST7	GCA_003606285.1	229155	229155	type	True	100.0	423	424	95	conclusive
Borrelia parkeri	strain=SLO	GCA_000568735.2	141	141	reftype	True	82.7115	285	424	95	below_threshold
Borrelia hermsii	strain=DAH	GCA_000012065.2	140	140	suspected-type	True	82.7004	291	424	95	below_threshold
Borrelia turicatae	strain=91E135	GCA_000012085.2	142	142	reftype	True	82.6952	280	424	95	below_threshold
Borrelia hermsii	strain=DAH	GCA_023035675.1	140	140	suspected-type	True	82.6814	295	424	95	below_threshold
Borrelia puertoricensis	strain=SUM	GCA_023035875.1	2756107	2756107	type	True	82.1852	288	424	95	below_threshold
Borrelia miyamotoi	strain=HT31	GCA_019668505.1	47466	47466	type	True	81.9858	265	424	95	below_threshold
Borrelia anserina	strain=Es	GCA_001936255.1	143	143	reftype	True	81.7273	278	424	95	below_threshold
Borrelia coriaceae	strain=ATCC 43381	GCA_000518125.1	144	144	type	True	81.4377	276	424	95	below_threshold
Borrelia coriaceae	strain=Co53	GCA_023035295.1	144	144	type	True	81.3417	286	424	95	below_threshold
Borrelia coriaceae	strain=Co53	GCA_000568755.1	144	144	type	True	81.3398	283	424	95	below_threshold
Borreliella burgdorferi	strain=FDAARGOS_196	GCA_002083055.2	139	139	type	True	78.2874	174	424	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:44:35,434] [INFO] DFAST Taxonomy check result was written to GCF_003606285.1_ASM360628v1_genomic.fna/tc_result.tsv
[2024-01-24 11:44:35,435] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:44:35,435] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:44:35,435] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgac277171-bfdf-4c79-8676-0208c5937951/dqc_reference/checkm_data
[2024-01-24 11:44:35,436] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:44:35,452] [INFO] Task started: CheckM
[2024-01-24 11:44:35,452] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003606285.1_ASM360628v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003606285.1_ASM360628v1_genomic.fna/checkm_input GCF_003606285.1_ASM360628v1_genomic.fna/checkm_result
[2024-01-24 11:44:51,600] [INFO] Task succeeded: CheckM
[2024-01-24 11:44:51,601] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:44:51,619] [INFO] ===== Completeness check finished =====
[2024-01-24 11:44:51,619] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:44:51,620] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003606285.1_ASM360628v1_genomic.fna/markers.fasta)
[2024-01-24 11:44:51,620] [INFO] Task started: Blastn
[2024-01-24 11:44:51,621] [INFO] Running command: blastn -query GCF_003606285.1_ASM360628v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgac277171-bfdf-4c79-8676-0208c5937951/dqc_reference/reference_markers_gtdb.fasta -out GCF_003606285.1_ASM360628v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:44:52,812] [INFO] Task succeeded: Blastn
[2024-01-24 11:44:52,815] [INFO] Selected 8 target genomes.
[2024-01-24 11:44:52,816] [INFO] Target genome list was writen to GCF_003606285.1_ASM360628v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:44:52,823] [INFO] Task started: fastANI
[2024-01-24 11:44:52,824] [INFO] Running command: fastANI --query /var/lib/cwl/stg14800fda-08b1-4e6f-b330-62390b988b0d/GCF_003606285.1_ASM360628v1_genomic.fna.gz --refList GCF_003606285.1_ASM360628v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003606285.1_ASM360628v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:44:55,381] [INFO] Task succeeded: fastANI
[2024-01-24 11:44:55,390] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:44:55,391] [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_003606285.1	s__Borrelia turcica	100.0	423	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_014084025.1	s__Borrelia sp014084025	88.885	333	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003076595.1	s__Borrelia tachyglossi	83.6833	304	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000012085.2	s__Borrelia turicatae	82.6952	280	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	97.95	97.47	0.93	0.89	4	-
GCF_001660005.1	s__Borrelia hermsii	82.6578	298	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	98.15	95.65	0.97	0.94	7	-
GCF_000445425.4	s__Borrelia miyamotoi	82.0585	256	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	97.85	96.70	1.00	0.96	22	-
GCF_001936255.1	s__Borrelia anserina	81.7273	278	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	99.99	99.99	0.97	0.97	2	-
GCF_000568755.1	s__Borrelia coriaceae	81.3398	283	424	d__Bacteria;p__Spirochaetota;c__Spirochaetia;o__Borreliales;f__Borreliaceae;g__Borrelia	95.0	99.88	99.88	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:44:55,392] [INFO] GTDB search result was written to GCF_003606285.1_ASM360628v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:44:55,393] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:44:55,396] [INFO] DFAST_QC result json was written to GCF_003606285.1_ASM360628v1_genomic.fna/dqc_result.json
[2024-01-24 11:44:55,396] [INFO] DFAST_QC completed!
[2024-01-24 11:44:55,397] [INFO] Total running time: 0h0m32s