[2024-01-25 18:53:20,659] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:53:20,661] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:53:20,661] [INFO] DQC Reference Directory: /var/lib/cwl/stgf54716b3-bec3-400c-be99-10d012d643ad/dqc_reference
[2024-01-25 18:53:21,771] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:53:21,772] [INFO] Task started: Prodigal
[2024-01-25 18:53:21,772] [INFO] Running command: gunzip -c /var/lib/cwl/stg4a6ffc00-ef8b-47f5-81af-1f79f557757b/GCF_009755265.1_ASM975526v1_genomic.fna.gz | prodigal -d GCF_009755265.1_ASM975526v1_genomic.fna/cds.fna -a GCF_009755265.1_ASM975526v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:53:29,379] [INFO] Task succeeded: Prodigal
[2024-01-25 18:53:29,380] [INFO] Task started: HMMsearch
[2024-01-25 18:53:29,380] [INFO] Running command: hmmsearch --tblout GCF_009755265.1_ASM975526v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf54716b3-bec3-400c-be99-10d012d643ad/dqc_reference/reference_markers.hmm GCF_009755265.1_ASM975526v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:53:29,599] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:53:29,600] [INFO] Found 6/6 markers.
[2024-01-25 18:53:29,632] [INFO] Query marker FASTA was written to GCF_009755265.1_ASM975526v1_genomic.fna/markers.fasta
[2024-01-25 18:53:29,632] [INFO] Task started: Blastn
[2024-01-25 18:53:29,633] [INFO] Running command: blastn -query GCF_009755265.1_ASM975526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf54716b3-bec3-400c-be99-10d012d643ad/dqc_reference/reference_markers.fasta -out GCF_009755265.1_ASM975526v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:53:30,318] [INFO] Task succeeded: Blastn
[2024-01-25 18:53:30,321] [INFO] Selected 6 target genomes.
[2024-01-25 18:53:30,322] [INFO] Target genome list was writen to GCF_009755265.1_ASM975526v1_genomic.fna/target_genomes.txt
[2024-01-25 18:53:30,333] [INFO] Task started: fastANI
[2024-01-25 18:53:30,333] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6ffc00-ef8b-47f5-81af-1f79f557757b/GCF_009755265.1_ASM975526v1_genomic.fna.gz --refList GCF_009755265.1_ASM975526v1_genomic.fna/target_genomes.txt --output GCF_009755265.1_ASM975526v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:53:34,939] [INFO] Task succeeded: fastANI
[2024-01-25 18:53:34,939] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf54716b3-bec3-400c-be99-10d012d643ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:53:34,940] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf54716b3-bec3-400c-be99-10d012d643ad/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:53:34,946] [INFO] Found 6 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:53:34,946] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:53:34,946] [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
Adlercreutzia hattorii	strain=8CFCBH1	GCA_011405655.1	2707299	2707299	type	True	97.0856	805	900	95	conclusive
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	94.3485	718	900	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_016865385.1	394340	446660	type	True	94.2953	683	900	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	94.2475	684	900	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_003428485.1	394340	446660	type	True	94.1555	661	900	95	below_threshold
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	94.1046	688	900	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:53:34,957] [INFO] DFAST Taxonomy check result was written to GCF_009755265.1_ASM975526v1_genomic.fna/tc_result.tsv
[2024-01-25 18:53:34,958] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:53:34,958] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:53:34,959] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf54716b3-bec3-400c-be99-10d012d643ad/dqc_reference/checkm_data
[2024-01-25 18:53:34,960] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:53:35,001] [INFO] Task started: CheckM
[2024-01-25 18:53:35,001] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009755265.1_ASM975526v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009755265.1_ASM975526v1_genomic.fna/checkm_input GCF_009755265.1_ASM975526v1_genomic.fna/checkm_result
[2024-01-25 18:54:00,186] [INFO] Task succeeded: CheckM
[2024-01-25 18:54:00,187] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:54:00,206] [INFO] ===== Completeness check finished =====
[2024-01-25 18:54:00,206] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:54:00,207] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009755265.1_ASM975526v1_genomic.fna/markers.fasta)
[2024-01-25 18:54:00,207] [INFO] Task started: Blastn
[2024-01-25 18:54:00,207] [INFO] Running command: blastn -query GCF_009755265.1_ASM975526v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf54716b3-bec3-400c-be99-10d012d643ad/dqc_reference/reference_markers_gtdb.fasta -out GCF_009755265.1_ASM975526v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:01,325] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:01,329] [INFO] Selected 8 target genomes.
[2024-01-25 18:54:01,329] [INFO] Target genome list was writen to GCF_009755265.1_ASM975526v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:54:01,340] [INFO] Task started: fastANI
[2024-01-25 18:54:01,341] [INFO] Running command: fastANI --query /var/lib/cwl/stg4a6ffc00-ef8b-47f5-81af-1f79f557757b/GCF_009755265.1_ASM975526v1_genomic.fna.gz --refList GCF_009755265.1_ASM975526v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009755265.1_ASM975526v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:54:07,009] [INFO] Task succeeded: fastANI
[2024-01-25 18:54:07,016] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:54:07,016] [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_011405655.1	s__Adlercreutzia celatus_A	97.0856	805	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	96.32	95.52	0.87	0.80	16	conclusive
GCF_000478885.1	s__Adlercreutzia equolifaciens	94.3485	718	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.05	95.56	0.84	0.79	7	-
GCF_008831045.1	s__Adlercreutzia muris	84.5742	552	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
GCF_000403355.2	s__Adlercreutzia caecimuris	84.5613	548	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.41	97.35	0.86	0.85	5	-
GCA_910589165.1	s__Adlercreutzia sp910589165	84.4208	517	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000422625.1	s__Adlercreutzia mucosicola	83.9656	547	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	-
GCA_910589695.1	s__QWKK01 sp910589695	81.0381	322	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__QWKK01	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013185065.1	s__CAAEEV01 sp013185065	80.8254	331	900	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__CAAEEV01	95.0	97.04	97.04	0.76	0.76	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:54:07,018] [INFO] GTDB search result was written to GCF_009755265.1_ASM975526v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:54:07,019] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:54:07,022] [INFO] DFAST_QC result json was written to GCF_009755265.1_ASM975526v1_genomic.fna/dqc_result.json
[2024-01-25 18:54:07,022] [INFO] DFAST_QC completed!
[2024-01-25 18:54:07,022] [INFO] Total running time: 0h0m46s