[2023-06-18 18:31:41,226] [INFO] DFAST_QC pipeline started.
[2023-06-18 18:31:41,229] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 18:31:41,229] [INFO] DQC Reference Directory: /var/lib/cwl/stg902b026f-448a-4a26-91ea-e8d972675189/dqc_reference
[2023-06-18 18:31:43,587] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 18:31:43,588] [INFO] Task started: Prodigal
[2023-06-18 18:31:43,589] [INFO] Running command: gunzip -c /var/lib/cwl/stg680884ed-49b1-4e9c-920d-c9a51781b7d0/GCA_018370815.1_ASM1837081v1_genomic.fna.gz | prodigal -d GCA_018370815.1_ASM1837081v1_genomic.fna/cds.fna -a GCA_018370815.1_ASM1837081v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 18:31:52,120] [INFO] Task succeeded: Prodigal
[2023-06-18 18:31:52,121] [INFO] Task started: HMMsearch
[2023-06-18 18:31:52,121] [INFO] Running command: hmmsearch --tblout GCA_018370815.1_ASM1837081v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg902b026f-448a-4a26-91ea-e8d972675189/dqc_reference/reference_markers.hmm GCA_018370815.1_ASM1837081v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 18:31:52,357] [INFO] Task succeeded: HMMsearch
[2023-06-18 18:31:52,358] [INFO] Found 6/6 markers.
[2023-06-18 18:31:52,390] [INFO] Query marker FASTA was written to GCA_018370815.1_ASM1837081v1_genomic.fna/markers.fasta
[2023-06-18 18:31:52,390] [INFO] Task started: Blastn
[2023-06-18 18:31:52,390] [INFO] Running command: blastn -query GCA_018370815.1_ASM1837081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg902b026f-448a-4a26-91ea-e8d972675189/dqc_reference/reference_markers.fasta -out GCA_018370815.1_ASM1837081v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:31:53,093] [INFO] Task succeeded: Blastn
[2023-06-18 18:31:53,098] [INFO] Selected 6 target genomes.
[2023-06-18 18:31:53,098] [INFO] Target genome list was writen to GCA_018370815.1_ASM1837081v1_genomic.fna/target_genomes.txt
[2023-06-18 18:31:53,100] [INFO] Task started: fastANI
[2023-06-18 18:31:53,100] [INFO] Running command: fastANI --query /var/lib/cwl/stg680884ed-49b1-4e9c-920d-c9a51781b7d0/GCA_018370815.1_ASM1837081v1_genomic.fna.gz --refList GCA_018370815.1_ASM1837081v1_genomic.fna/target_genomes.txt --output GCA_018370815.1_ASM1837081v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 18:31:57,106] [INFO] Task succeeded: fastANI
[2023-06-18 18:31:57,107] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg902b026f-448a-4a26-91ea-e8d972675189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 18:31:57,107] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg902b026f-448a-4a26-91ea-e8d972675189/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 18:31:57,115] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2023-06-18 18:31:57,115] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2023-06-18 18:31:57,115] [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	95.399	735	921	95	inconclusive
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_003726015.1	394340	446660	type	True	95.3958	689	921	95	inconclusive
Adlercreutzia equolifaciens subsp. celatus	strain=DSM 18785	GCA_024171685.1	394340	446660	type	True	95.3897	695	921	95	inconclusive
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_003428485.1	394340	446660	type	True	95.359	666	921	95	inconclusive
Adlercreutzia equolifaciens subsp. equolifaciens	strain=DSM 19450	GCA_000478885.1	2864143	446660	type	True	95.3347	702	921	95	inconclusive
Adlercreutzia equolifaciens subsp. celatus	strain=JCM 14811	GCA_016865385.1	394340	446660	type	True	95.3196	705	921	95	inconclusive
--------------------------------------------------------------------------------
[2023-06-18 18:31:57,117] [INFO] DFAST Taxonomy check result was written to GCA_018370815.1_ASM1837081v1_genomic.fna/tc_result.tsv
[2023-06-18 18:31:57,124] [INFO] ===== Taxonomy check completed =====
[2023-06-18 18:31:57,125] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 18:31:57,125] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg902b026f-448a-4a26-91ea-e8d972675189/dqc_reference/checkm_data
[2023-06-18 18:31:57,126] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 18:31:57,156] [INFO] Task started: CheckM
[2023-06-18 18:31:57,156] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_018370815.1_ASM1837081v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_018370815.1_ASM1837081v1_genomic.fna/checkm_input GCA_018370815.1_ASM1837081v1_genomic.fna/checkm_result
[2023-06-18 18:32:25,622] [INFO] Task succeeded: CheckM
[2023-06-18 18:32:25,624] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-18 18:32:25,658] [INFO] ===== Completeness check finished =====
[2023-06-18 18:32:25,658] [INFO] ===== Start GTDB Search =====
[2023-06-18 18:32:25,658] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_018370815.1_ASM1837081v1_genomic.fna/markers.fasta)
[2023-06-18 18:32:25,659] [INFO] Task started: Blastn
[2023-06-18 18:32:25,659] [INFO] Running command: blastn -query GCA_018370815.1_ASM1837081v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg902b026f-448a-4a26-91ea-e8d972675189/dqc_reference/reference_markers_gtdb.fasta -out GCA_018370815.1_ASM1837081v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 18:32:26,859] [INFO] Task succeeded: Blastn
[2023-06-18 18:32:26,864] [INFO] Selected 6 target genomes.
[2023-06-18 18:32:26,864] [INFO] Target genome list was writen to GCA_018370815.1_ASM1837081v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 18:32:26,866] [INFO] Task started: fastANI
[2023-06-18 18:32:26,866] [INFO] Running command: fastANI --query /var/lib/cwl/stg680884ed-49b1-4e9c-920d-c9a51781b7d0/GCA_018370815.1_ASM1837081v1_genomic.fna.gz --refList GCA_018370815.1_ASM1837081v1_genomic.fna/target_genomes_gtdb.txt --output GCA_018370815.1_ASM1837081v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 18:32:31,162] [INFO] Task succeeded: fastANI
[2023-06-18 18:32:31,170] [INFO] Found 6 fastANI hits (2 hits with ANI > circumscription radius)
[2023-06-18 18:32:31,170] [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	95.399	735	921	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	96.32	95.52	0.87	0.80	16	inconclusive
GCF_000478885.1	s__Adlercreutzia equolifaciens	95.3347	702	921	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.05	95.56	0.84	0.79	7	inconclusive
GCF_000403355.2	s__Adlercreutzia caecimuris	84.496	551	921	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	84.4711	511	921	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008831045.1	s__Adlercreutzia muris	84.4562	545	921	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	-
GCF_000422625.1	s__Adlercreutzia mucosicola	84.0362	522	921	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	-
--------------------------------------------------------------------------------
[2023-06-18 18:32:31,172] [INFO] GTDB search result was written to GCA_018370815.1_ASM1837081v1_genomic.fna/result_gtdb.tsv
[2023-06-18 18:32:31,173] [INFO] ===== GTDB Search completed =====
[2023-06-18 18:32:31,176] [INFO] DFAST_QC result json was written to GCA_018370815.1_ASM1837081v1_genomic.fna/dqc_result.json
[2023-06-18 18:32:31,176] [INFO] DFAST_QC completed!
[2023-06-18 18:32:31,176] [INFO] Total running time: 0h0m50s