[2024-01-25 19:42:50,951] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:42:50,952] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:42:50,953] [INFO] DQC Reference Directory: /var/lib/cwl/stgf755968c-2f8a-47de-85e2-0282e6649e2f/dqc_reference
[2024-01-25 19:42:52,050] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:42:52,050] [INFO] Task started: Prodigal
[2024-01-25 19:42:52,050] [INFO] Running command: gunzip -c /var/lib/cwl/stg4837e19f-acc8-4f54-9707-b0ae7c292e45/GCF_030811535.1_ASM3081153v1_genomic.fna.gz | prodigal -d GCF_030811535.1_ASM3081153v1_genomic.fna/cds.fna -a GCF_030811535.1_ASM3081153v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:42:57,290] [INFO] Task succeeded: Prodigal
[2024-01-25 19:42:57,290] [INFO] Task started: HMMsearch
[2024-01-25 19:42:57,290] [INFO] Running command: hmmsearch --tblout GCF_030811535.1_ASM3081153v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf755968c-2f8a-47de-85e2-0282e6649e2f/dqc_reference/reference_markers.hmm GCF_030811535.1_ASM3081153v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:42:57,467] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:42:57,468] [INFO] Found 6/6 markers.
[2024-01-25 19:42:57,487] [INFO] Query marker FASTA was written to GCF_030811535.1_ASM3081153v1_genomic.fna/markers.fasta
[2024-01-25 19:42:57,487] [INFO] Task started: Blastn
[2024-01-25 19:42:57,487] [INFO] Running command: blastn -query GCF_030811535.1_ASM3081153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf755968c-2f8a-47de-85e2-0282e6649e2f/dqc_reference/reference_markers.fasta -out GCF_030811535.1_ASM3081153v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:42:58,094] [INFO] Task succeeded: Blastn
[2024-01-25 19:42:58,097] [INFO] Selected 30 target genomes.
[2024-01-25 19:42:58,098] [INFO] Target genome list was writen to GCF_030811535.1_ASM3081153v1_genomic.fna/target_genomes.txt
[2024-01-25 19:42:58,129] [INFO] Task started: fastANI
[2024-01-25 19:42:58,129] [INFO] Running command: fastANI --query /var/lib/cwl/stg4837e19f-acc8-4f54-9707-b0ae7c292e45/GCF_030811535.1_ASM3081153v1_genomic.fna.gz --refList GCF_030811535.1_ASM3081153v1_genomic.fna/target_genomes.txt --output GCF_030811535.1_ASM3081153v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:43:15,450] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:15,451] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf755968c-2f8a-47de-85e2-0282e6649e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:43:15,451] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf755968c-2f8a-47de-85e2-0282e6649e2f/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:43:15,457] [INFO] Found 6 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:43:15,457] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:43:15,457] [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
Trueperella bialowiezensis	strain=NCTC13354	GCA_900637955.1	312285	312285	type	True	78.313	198	634	95	below_threshold
Arcanobacterium haemolyticum	strain=DSM 20595	GCA_000092365.1	28264	28264	type	True	77.994	50	634	95	below_threshold
Trueperella pecoris	strain=19M2397	GCA_014926385.1	2733571	2733571	type	True	77.9742	127	634	95	below_threshold
Trueperella pyogenes	strain=NCTC5224	GCA_900460345.1	1661	1661	type	True	77.8615	117	634	95	below_threshold
Trueperella pyogenes	strain=DSM 20630	GCA_014191445.1	1661	1661	type	True	77.5807	108	634	95	below_threshold
Trueperella bernardiae	strain=LCDC 89-0504	GCA_001469025.1	59561	59561	type	True	77.5395	138	634	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:43:15,458] [INFO] DFAST Taxonomy check result was written to GCF_030811535.1_ASM3081153v1_genomic.fna/tc_result.tsv
[2024-01-25 19:43:15,459] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:43:15,459] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:43:15,459] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf755968c-2f8a-47de-85e2-0282e6649e2f/dqc_reference/checkm_data
[2024-01-25 19:43:15,460] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:43:15,485] [INFO] Task started: CheckM
[2024-01-25 19:43:15,485] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030811535.1_ASM3081153v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030811535.1_ASM3081153v1_genomic.fna/checkm_input GCF_030811535.1_ASM3081153v1_genomic.fna/checkm_result
[2024-01-25 19:43:35,622] [INFO] Task succeeded: CheckM
[2024-01-25 19:43:35,623] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:43:35,640] [INFO] ===== Completeness check finished =====
[2024-01-25 19:43:35,641] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:43:35,641] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030811535.1_ASM3081153v1_genomic.fna/markers.fasta)
[2024-01-25 19:43:35,641] [INFO] Task started: Blastn
[2024-01-25 19:43:35,641] [INFO] Running command: blastn -query GCF_030811535.1_ASM3081153v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf755968c-2f8a-47de-85e2-0282e6649e2f/dqc_reference/reference_markers_gtdb.fasta -out GCF_030811535.1_ASM3081153v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:36,549] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:36,552] [INFO] Selected 31 target genomes.
[2024-01-25 19:43:36,552] [INFO] Target genome list was writen to GCF_030811535.1_ASM3081153v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:43:36,584] [INFO] Task started: fastANI
[2024-01-25 19:43:36,584] [INFO] Running command: fastANI --query /var/lib/cwl/stg4837e19f-acc8-4f54-9707-b0ae7c292e45/GCF_030811535.1_ASM3081153v1_genomic.fna.gz --refList GCF_030811535.1_ASM3081153v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030811535.1_ASM3081153v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:43:54,435] [INFO] Task succeeded: fastANI
[2024-01-25 19:43:54,441] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-25 19:43:54,441] [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_900637955.1	s__Trueperella bialowiezensis	78.3132	198	634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000092365.1	s__Arcanobacterium haemolyticum	78.0966	51	634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	99.39	98.67	0.98	0.96	4	-
GCF_014926385.1	s__Trueperella pecoris	78.0294	127	634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	97.88	95.38	0.92	0.88	4	-
GCA_012727825.1	s__Trueperella sp012727825	77.8186	126	634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900460345.1	s__Trueperella pyogenes	77.6168	115	634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	98.61	97.91	0.94	0.87	20	-
GCF_001469025.1	s__Trueperella bernardiae	77.5395	138	634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Trueperella	95.0	99.54	99.43	0.95	0.94	5	-
GCA_012516575.1	s__Arcanobacterium sp012516575	76.8213	50	634	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Actinomycetaceae;g__Arcanobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:43:54,443] [INFO] GTDB search result was written to GCF_030811535.1_ASM3081153v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:43:54,444] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:43:54,447] [INFO] DFAST_QC result json was written to GCF_030811535.1_ASM3081153v1_genomic.fna/dqc_result.json
[2024-01-25 19:43:54,447] [INFO] DFAST_QC completed!
[2024-01-25 19:43:54,447] [INFO] Total running time: 0h1m3s