[2024-01-24 12:37:25,068] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:37:25,072] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:37:25,074] [INFO] DQC Reference Directory: /var/lib/cwl/stg1b049255-23d5-4d35-b262-d537eee3ed97/dqc_reference
[2024-01-24 12:37:26,428] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:37:26,428] [INFO] Task started: Prodigal
[2024-01-24 12:37:26,429] [INFO] Running command: gunzip -c /var/lib/cwl/stg3765595f-3c9f-49de-a991-c875c0d1829f/GCF_005518285.1_ASM551828v1_genomic.fna.gz | prodigal -d GCF_005518285.1_ASM551828v1_genomic.fna/cds.fna -a GCF_005518285.1_ASM551828v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:37:30,434] [INFO] Task succeeded: Prodigal
[2024-01-24 12:37:30,434] [INFO] Task started: HMMsearch
[2024-01-24 12:37:30,434] [INFO] Running command: hmmsearch --tblout GCF_005518285.1_ASM551828v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1b049255-23d5-4d35-b262-d537eee3ed97/dqc_reference/reference_markers.hmm GCF_005518285.1_ASM551828v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:37:30,676] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:37:30,678] [WARNING] Found 4/6 markers. [/var/lib/cwl/stg3765595f-3c9f-49de-a991-c875c0d1829f/GCF_005518285.1_ASM551828v1_genomic.fna.gz]
[2024-01-24 12:37:30,704] [INFO] Query marker FASTA was written to GCF_005518285.1_ASM551828v1_genomic.fna/markers.fasta
[2024-01-24 12:37:30,704] [INFO] Task started: Blastn
[2024-01-24 12:37:30,704] [INFO] Running command: blastn -query GCF_005518285.1_ASM551828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b049255-23d5-4d35-b262-d537eee3ed97/dqc_reference/reference_markers.fasta -out GCF_005518285.1_ASM551828v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:31,291] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:31,296] [INFO] Selected 7 target genomes.
[2024-01-24 12:37:31,296] [INFO] Target genome list was writen to GCF_005518285.1_ASM551828v1_genomic.fna/target_genomes.txt
[2024-01-24 12:37:31,352] [INFO] Task started: fastANI
[2024-01-24 12:37:31,352] [INFO] Running command: fastANI --query /var/lib/cwl/stg3765595f-3c9f-49de-a991-c875c0d1829f/GCF_005518285.1_ASM551828v1_genomic.fna.gz --refList GCF_005518285.1_ASM551828v1_genomic.fna/target_genomes.txt --output GCF_005518285.1_ASM551828v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:37:35,359] [INFO] Task succeeded: fastANI
[2024-01-24 12:37:35,360] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1b049255-23d5-4d35-b262-d537eee3ed97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:37:35,361] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1b049255-23d5-4d35-b262-d537eee3ed97/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:37:35,367] [INFO] Found 5 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:37:35,367] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:37:35,367] [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
Brachyspira catarrhinii	strain=Z12	GCA_005518285.1	2528966	2528966	type	True	100.0	521	529	95	conclusive
Brachyspira aalborgi	strain=513A	GCA_008016455.1	29522	29522	type	True	84.7128	422	529	95	below_threshold
Brachyspira alvinipulli	strain=ATCC 51933	GCA_000518245.1	84379	84379	type	True	76.1674	127	529	95	below_threshold
Brachyspira suanatina	strain=AN4859/03	GCA_001049755.1	381802	381802	type	True	75.962	135	529	95	below_threshold
Brachyspira pilosicoli	strain=P43/6/78	GCA_000325665.1	52584	52584	type	True	75.9425	118	529	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:37:35,370] [INFO] DFAST Taxonomy check result was written to GCF_005518285.1_ASM551828v1_genomic.fna/tc_result.tsv
[2024-01-24 12:37:35,370] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:37:35,370] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:37:35,371] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1b049255-23d5-4d35-b262-d537eee3ed97/dqc_reference/checkm_data
[2024-01-24 12:37:35,372] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:37:35,406] [INFO] Task started: CheckM
[2024-01-24 12:37:35,407] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_005518285.1_ASM551828v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_005518285.1_ASM551828v1_genomic.fna/checkm_input GCF_005518285.1_ASM551828v1_genomic.fna/checkm_result
[2024-01-24 12:37:54,822] [INFO] Task succeeded: CheckM
[2024-01-24 12:37:54,823] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 77.28%
Contamintation: 0.52%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:37:54,841] [INFO] ===== Completeness check finished =====
[2024-01-24 12:37:54,842] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:37:54,842] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_005518285.1_ASM551828v1_genomic.fna/markers.fasta)
[2024-01-24 12:37:54,843] [INFO] Task started: Blastn
[2024-01-24 12:37:54,843] [INFO] Running command: blastn -query GCF_005518285.1_ASM551828v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1b049255-23d5-4d35-b262-d537eee3ed97/dqc_reference/reference_markers_gtdb.fasta -out GCF_005518285.1_ASM551828v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:37:55,617] [INFO] Task succeeded: Blastn
[2024-01-24 12:37:55,627] [INFO] Selected 12 target genomes.
[2024-01-24 12:37:55,627] [INFO] Target genome list was writen to GCF_005518285.1_ASM551828v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:37:55,655] [INFO] Task started: fastANI
[2024-01-24 12:37:55,656] [INFO] Running command: fastANI --query /var/lib/cwl/stg3765595f-3c9f-49de-a991-c875c0d1829f/GCF_005518285.1_ASM551828v1_genomic.fna.gz --refList GCF_005518285.1_ASM551828v1_genomic.fna/target_genomes_gtdb.txt --output GCF_005518285.1_ASM551828v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:38:02,003] [INFO] Task succeeded: fastANI
[2024-01-24 12:38:02,016] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:38:02,016] [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_005518285.1	s__Brachyspira catarrhinii	100.0	521	529	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_008016455.1	s__Brachyspira aalborgi	84.7588	419	529	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	95.81	95.36	0.82	0.78	21	-
GCA_910588665.1	s__Brachyspira sp910588665	76.1811	122	529	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000518245.1	s__Brachyspira alvinipulli	76.1672	127	529	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910578695.1	s__Brachyspira sp910578695	76.083	116	529	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001049755.1	s__Brachyspira suanatina	75.962	135	529	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000325665.1	s__Brachyspira pilosicoli	75.9538	117	529	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	98.38	97.84	0.95	0.91	19	-
--------------------------------------------------------------------------------
[2024-01-24 12:38:02,018] [INFO] GTDB search result was written to GCF_005518285.1_ASM551828v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:38:02,018] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:38:02,021] [INFO] DFAST_QC result json was written to GCF_005518285.1_ASM551828v1_genomic.fna/dqc_result.json
[2024-01-24 12:38:02,021] [INFO] DFAST_QC completed!
[2024-01-24 12:38:02,021] [INFO] Total running time: 0h0m37s