[2024-01-24 13:18:41,816] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:18:41,818] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:18:41,819] [INFO] DQC Reference Directory: /var/lib/cwl/stg62c2598b-c6b9-4ebd-b844-c4b352bdbcce/dqc_reference
[2024-01-24 13:18:43,293] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:18:43,294] [INFO] Task started: Prodigal
[2024-01-24 13:18:43,294] [INFO] Running command: gunzip -c /var/lib/cwl/stgb2e2743f-37f4-45af-8c38-158d9cba2e50/GCF_008016455.1_ASM801645v1_genomic.fna.gz | prodigal -d GCF_008016455.1_ASM801645v1_genomic.fna/cds.fna -a GCF_008016455.1_ASM801645v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:47,383] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:47,383] [INFO] Task started: HMMsearch
[2024-01-24 13:18:47,383] [INFO] Running command: hmmsearch --tblout GCF_008016455.1_ASM801645v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg62c2598b-c6b9-4ebd-b844-c4b352bdbcce/dqc_reference/reference_markers.hmm GCF_008016455.1_ASM801645v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:47,645] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:47,646] [INFO] Found 6/6 markers.
[2024-01-24 13:18:47,673] [INFO] Query marker FASTA was written to GCF_008016455.1_ASM801645v1_genomic.fna/markers.fasta
[2024-01-24 13:18:47,673] [INFO] Task started: Blastn
[2024-01-24 13:18:47,674] [INFO] Running command: blastn -query GCF_008016455.1_ASM801645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c2598b-c6b9-4ebd-b844-c4b352bdbcce/dqc_reference/reference_markers.fasta -out GCF_008016455.1_ASM801645v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:48,415] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:48,419] [INFO] Selected 13 target genomes.
[2024-01-24 13:18:48,419] [INFO] Target genome list was writen to GCF_008016455.1_ASM801645v1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:48,440] [INFO] Task started: fastANI
[2024-01-24 13:18:48,440] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e2743f-37f4-45af-8c38-158d9cba2e50/GCF_008016455.1_ASM801645v1_genomic.fna.gz --refList GCF_008016455.1_ASM801645v1_genomic.fna/target_genomes.txt --output GCF_008016455.1_ASM801645v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:55,804] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:55,804] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg62c2598b-c6b9-4ebd-b844-c4b352bdbcce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:55,805] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg62c2598b-c6b9-4ebd-b844-c4b352bdbcce/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:55,813] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:18:55,814] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:18:55,814] [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 aalborgi	strain=513A	GCA_008016455.1	29522	29522	type	True	100.0	831	831	95	conclusive
Brachyspira catarrhinii	strain=Z12	GCA_005518285.1	2528966	2528966	type	True	84.8243	421	831	95	below_threshold
Brachyspira hyodysenteriae	strain=B-78	GCA_001676785.2	159	159	type	True	76.929	279	831	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_000383255.1	159	159	type	True	76.9043	283	831	95	below_threshold
Brachyspira hyodysenteriae	strain=B78	GCA_001013005.1	159	159	type	True	76.873	290	831	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_002214805.1	1287055	1287055	type	True	76.6374	312	831	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_001746225.1	1287055	1287055	type	True	76.5937	305	831	95	below_threshold
Brachyspira pilosicoli	strain=P43/6/78	GCA_000325665.1	52584	52584	type	True	76.5588	274	831	95	below_threshold
Brachyspira alvinipulli	strain=ATCC 51933	GCA_000518245.1	84379	84379	type	True	76.4756	309	831	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:55,816] [INFO] DFAST Taxonomy check result was written to GCF_008016455.1_ASM801645v1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:55,816] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:55,817] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:55,817] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg62c2598b-c6b9-4ebd-b844-c4b352bdbcce/dqc_reference/checkm_data
[2024-01-24 13:18:55,820] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:55,851] [INFO] Task started: CheckM
[2024-01-24 13:18:55,851] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008016455.1_ASM801645v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008016455.1_ASM801645v1_genomic.fna/checkm_input GCF_008016455.1_ASM801645v1_genomic.fna/checkm_result
[2024-01-24 13:19:15,253] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:15,255] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:15,276] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:15,277] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:15,277] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008016455.1_ASM801645v1_genomic.fna/markers.fasta)
[2024-01-24 13:19:15,278] [INFO] Task started: Blastn
[2024-01-24 13:19:15,278] [INFO] Running command: blastn -query GCF_008016455.1_ASM801645v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg62c2598b-c6b9-4ebd-b844-c4b352bdbcce/dqc_reference/reference_markers_gtdb.fasta -out GCF_008016455.1_ASM801645v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:16,189] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:16,193] [INFO] Selected 15 target genomes.
[2024-01-24 13:19:16,193] [INFO] Target genome list was writen to GCF_008016455.1_ASM801645v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:16,207] [INFO] Task started: fastANI
[2024-01-24 13:19:16,207] [INFO] Running command: fastANI --query /var/lib/cwl/stgb2e2743f-37f4-45af-8c38-158d9cba2e50/GCF_008016455.1_ASM801645v1_genomic.fna.gz --refList GCF_008016455.1_ASM801645v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008016455.1_ASM801645v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:24,065] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:24,075] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:24,076] [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_008016455.1	s__Brachyspira aalborgi	100.0	831	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	95.81	95.36	0.82	0.78	21	conclusive
GCF_005518285.1	s__Brachyspira catarrhinii	84.8469	420	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910588665.1	s__Brachyspira sp910588665	76.9911	268	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001676785.2	s__Brachyspira hyodysenteriae	76.9025	282	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.16	98.93	0.98	0.95	58	-
GCF_001746205.1	s__Brachyspira hampsonii_B	76.8131	303	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002379365.1	s__Brachyspira sp002379365	76.8075	287	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002214805.1	s__Brachyspira hampsonii	76.6642	308	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.94	99.90	1.00	1.00	3	-
GCF_000223215.1	s__Brachyspira intermedia	76.6218	310	831	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009755885.1	s__Brachyspira sp009755885	76.6077	280	831	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	76.5595	274	831	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 13:19:24,077] [INFO] GTDB search result was written to GCF_008016455.1_ASM801645v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:24,078] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:24,081] [INFO] DFAST_QC result json was written to GCF_008016455.1_ASM801645v1_genomic.fna/dqc_result.json
[2024-01-24 13:19:24,081] [INFO] DFAST_QC completed!
[2024-01-24 13:19:24,081] [INFO] Total running time: 0h0m42s