[2024-01-24 14:06:59,790] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:06:59,793] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:06:59,793] [INFO] DQC Reference Directory: /var/lib/cwl/stg2301adeb-6c3f-4a1a-80e3-6294c5ef6c7d/dqc_reference
[2024-01-24 14:07:01,083] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:07:01,084] [INFO] Task started: Prodigal
[2024-01-24 14:07:01,084] [INFO] Running command: gunzip -c /var/lib/cwl/stge2901d6a-1863-40c8-aee7-c8451a99dc56/GCF_001676785.2_ASM167678v2_genomic.fna.gz | prodigal -d GCF_001676785.2_ASM167678v2_genomic.fna/cds.fna -a GCF_001676785.2_ASM167678v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:07:06,072] [INFO] Task succeeded: Prodigal
[2024-01-24 14:07:06,072] [INFO] Task started: HMMsearch
[2024-01-24 14:07:06,072] [INFO] Running command: hmmsearch --tblout GCF_001676785.2_ASM167678v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2301adeb-6c3f-4a1a-80e3-6294c5ef6c7d/dqc_reference/reference_markers.hmm GCF_001676785.2_ASM167678v2_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:07:06,268] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:07:06,269] [INFO] Found 6/6 markers.
[2024-01-24 14:07:06,294] [INFO] Query marker FASTA was written to GCF_001676785.2_ASM167678v2_genomic.fna/markers.fasta
[2024-01-24 14:07:06,295] [INFO] Task started: Blastn
[2024-01-24 14:07:06,295] [INFO] Running command: blastn -query GCF_001676785.2_ASM167678v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2301adeb-6c3f-4a1a-80e3-6294c5ef6c7d/dqc_reference/reference_markers.fasta -out GCF_001676785.2_ASM167678v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:06,848] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:06,856] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:06,856] [INFO] Target genome list was writen to GCF_001676785.2_ASM167678v2_genomic.fna/target_genomes.txt
[2024-01-24 14:07:06,866] [INFO] Task started: fastANI
[2024-01-24 14:07:06,866] [INFO] Running command: fastANI --query /var/lib/cwl/stge2901d6a-1863-40c8-aee7-c8451a99dc56/GCF_001676785.2_ASM167678v2_genomic.fna.gz --refList GCF_001676785.2_ASM167678v2_genomic.fna/target_genomes.txt --output GCF_001676785.2_ASM167678v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:07:14,478] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:14,478] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2301adeb-6c3f-4a1a-80e3-6294c5ef6c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:07:14,479] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2301adeb-6c3f-4a1a-80e3-6294c5ef6c7d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:07:14,486] [INFO] Found 7 fastANI hits (3 hits with ANI > threshold)
[2024-01-24 14:07:14,486] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:07:14,486] [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 hyodysenteriae	strain=B-78	GCA_001676785.2	159	159	type	True	100.0	1023	1023	95	conclusive
Brachyspira hyodysenteriae	strain=B78	GCA_001013005.1	159	159	type	True	99.9551	978	1023	95	conclusive
Brachyspira hyodysenteriae	strain=B78	GCA_000383255.1	159	159	type	True	99.9548	992	1023	95	conclusive
Brachyspira suanatina	strain=AN4859/03	GCA_001049755.1	381802	381802	type	True	92.8532	930	1023	95	below_threshold
Brachyspira intermedia	strain=PWS/A	GCA_000223215.1	84377	84377	type	True	91.7739	898	1023	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_002214805.1	1287055	1287055	type	True	88.6243	878	1023	95	below_threshold
Brachyspira hampsonii	strain=NSH-16	GCA_001746225.1	1287055	1287055	type	True	88.6187	843	1023	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:07:14,488] [INFO] DFAST Taxonomy check result was written to GCF_001676785.2_ASM167678v2_genomic.fna/tc_result.tsv
[2024-01-24 14:07:14,488] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:07:14,488] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:07:14,489] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2301adeb-6c3f-4a1a-80e3-6294c5ef6c7d/dqc_reference/checkm_data
[2024-01-24 14:07:14,490] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:07:14,519] [INFO] Task started: CheckM
[2024-01-24 14:07:14,519] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001676785.2_ASM167678v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001676785.2_ASM167678v2_genomic.fna/checkm_input GCF_001676785.2_ASM167678v2_genomic.fna/checkm_result
[2024-01-24 14:07:35,005] [INFO] Task succeeded: CheckM
[2024-01-24 14:07:35,007] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:07:35,024] [INFO] ===== Completeness check finished =====
[2024-01-24 14:07:35,024] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:07:35,025] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001676785.2_ASM167678v2_genomic.fna/markers.fasta)
[2024-01-24 14:07:35,025] [INFO] Task started: Blastn
[2024-01-24 14:07:35,025] [INFO] Running command: blastn -query GCF_001676785.2_ASM167678v2_genomic.fna/markers.fasta -db /var/lib/cwl/stg2301adeb-6c3f-4a1a-80e3-6294c5ef6c7d/dqc_reference/reference_markers_gtdb.fasta -out GCF_001676785.2_ASM167678v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:07:35,790] [INFO] Task succeeded: Blastn
[2024-01-24 14:07:35,793] [INFO] Selected 7 target genomes.
[2024-01-24 14:07:35,793] [INFO] Target genome list was writen to GCF_001676785.2_ASM167678v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:07:35,798] [INFO] Task started: fastANI
[2024-01-24 14:07:35,798] [INFO] Running command: fastANI --query /var/lib/cwl/stge2901d6a-1863-40c8-aee7-c8451a99dc56/GCF_001676785.2_ASM167678v2_genomic.fna.gz --refList GCF_001676785.2_ASM167678v2_genomic.fna/target_genomes_gtdb.txt --output GCF_001676785.2_ASM167678v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:07:43,130] [INFO] Task succeeded: fastANI
[2024-01-24 14:07:43,137] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:07:43,137] [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_001676785.2	s__Brachyspira hyodysenteriae	100.0	1023	1023	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.16	98.93	0.98	0.95	58	conclusive
GCF_001049755.1	s__Brachyspira suanatina	92.8532	930	1023	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000223215.1	s__Brachyspira intermedia	91.78	897	1023	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	88.6276	877	1023	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	99.94	99.90	1.00	1.00	3	-
GCF_001746205.1	s__Brachyspira hampsonii_B	88.1792	854	1023	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000316195.1	s__Brachyspira hampsonii_C	87.9782	849	1023	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	98.70	97.44	0.97	0.94	3	-
GCF_000518245.1	s__Brachyspira alvinipulli	84.5187	761	1023	d__Bacteria;p__Spirochaetota;c__Brachyspirae;o__Brachyspirales;f__Brachyspiraceae;g__Brachyspira	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:07:43,138] [INFO] GTDB search result was written to GCF_001676785.2_ASM167678v2_genomic.fna/result_gtdb.tsv
[2024-01-24 14:07:43,139] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:07:43,142] [INFO] DFAST_QC result json was written to GCF_001676785.2_ASM167678v2_genomic.fna/dqc_result.json
[2024-01-24 14:07:43,142] [INFO] DFAST_QC completed!
[2024-01-24 14:07:43,142] [INFO] Total running time: 0h0m43s