[2024-01-24 12:21:44,219] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:21:44,222] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:21:44,222] [INFO] DQC Reference Directory: /var/lib/cwl/stge77f07d7-7550-4e53-983d-bd710e916764/dqc_reference
[2024-01-24 12:21:45,730] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:21:45,731] [INFO] Task started: Prodigal
[2024-01-24 12:21:45,731] [INFO] Running command: gunzip -c /var/lib/cwl/stg838e92ec-2ed4-4b4e-93a8-42788e975fd8/GCF_000024225.1_ASM2422v1_genomic.fna.gz | prodigal -d GCF_000024225.1_ASM2422v1_genomic.fna/cds.fna -a GCF_000024225.1_ASM2422v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:21:49,966] [INFO] Task succeeded: Prodigal
[2024-01-24 12:21:49,967] [INFO] Task started: HMMsearch
[2024-01-24 12:21:49,967] [INFO] Running command: hmmsearch --tblout GCF_000024225.1_ASM2422v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge77f07d7-7550-4e53-983d-bd710e916764/dqc_reference/reference_markers.hmm GCF_000024225.1_ASM2422v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:21:50,194] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:21:50,195] [INFO] Found 6/6 markers.
[2024-01-24 12:21:50,213] [INFO] Query marker FASTA was written to GCF_000024225.1_ASM2422v1_genomic.fna/markers.fasta
[2024-01-24 12:21:50,214] [INFO] Task started: Blastn
[2024-01-24 12:21:50,214] [INFO] Running command: blastn -query GCF_000024225.1_ASM2422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77f07d7-7550-4e53-983d-bd710e916764/dqc_reference/reference_markers.fasta -out GCF_000024225.1_ASM2422v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:21:50,833] [INFO] Task succeeded: Blastn
[2024-01-24 12:21:50,837] [INFO] Selected 17 target genomes.
[2024-01-24 12:21:50,837] [INFO] Target genome list was writen to GCF_000024225.1_ASM2422v1_genomic.fna/target_genomes.txt
[2024-01-24 12:21:50,859] [INFO] Task started: fastANI
[2024-01-24 12:21:50,859] [INFO] Running command: fastANI --query /var/lib/cwl/stg838e92ec-2ed4-4b4e-93a8-42788e975fd8/GCF_000024225.1_ASM2422v1_genomic.fna.gz --refList GCF_000024225.1_ASM2422v1_genomic.fna/target_genomes.txt --output GCF_000024225.1_ASM2422v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:21:59,394] [INFO] Task succeeded: fastANI
[2024-01-24 12:21:59,394] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge77f07d7-7550-4e53-983d-bd710e916764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:21:59,394] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge77f07d7-7550-4e53-983d-bd710e916764/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:21:59,400] [INFO] Found 4 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:21:59,401] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:21:59,401] [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
Lancefieldella parvula	strain=DSM 20469	GCA_000024225.1	1382	1382	type	True	100.0	514	514	95	conclusive
Lancefieldella rimae	strain=DSM 7090	GCA_001438885.1	1383	1383	type	True	80.625	116	514	95	below_threshold
Lancefieldella rimae	strain=ATCC 49626	GCA_000174015.1	1383	1383	type	True	80.5296	116	514	95	below_threshold
Atopobium fossor	strain=DSM 15642	GCA_000483125.1	39487	39487	type	True	77.2615	55	514	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:21:59,402] [INFO] DFAST Taxonomy check result was written to GCF_000024225.1_ASM2422v1_genomic.fna/tc_result.tsv
[2024-01-24 12:21:59,403] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:21:59,403] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:21:59,403] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge77f07d7-7550-4e53-983d-bd710e916764/dqc_reference/checkm_data
[2024-01-24 12:21:59,404] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:21:59,430] [INFO] Task started: CheckM
[2024-01-24 12:21:59,430] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000024225.1_ASM2422v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000024225.1_ASM2422v1_genomic.fna/checkm_input GCF_000024225.1_ASM2422v1_genomic.fna/checkm_result
[2024-01-24 12:22:18,849] [INFO] Task succeeded: CheckM
[2024-01-24 12:22:18,851] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:22:18,875] [INFO] ===== Completeness check finished =====
[2024-01-24 12:22:18,876] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:22:18,876] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000024225.1_ASM2422v1_genomic.fna/markers.fasta)
[2024-01-24 12:22:18,877] [INFO] Task started: Blastn
[2024-01-24 12:22:18,877] [INFO] Running command: blastn -query GCF_000024225.1_ASM2422v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge77f07d7-7550-4e53-983d-bd710e916764/dqc_reference/reference_markers_gtdb.fasta -out GCF_000024225.1_ASM2422v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:22:19,790] [INFO] Task succeeded: Blastn
[2024-01-24 12:22:19,793] [INFO] Selected 8 target genomes.
[2024-01-24 12:22:19,794] [INFO] Target genome list was writen to GCF_000024225.1_ASM2422v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:22:19,800] [INFO] Task started: fastANI
[2024-01-24 12:22:19,800] [INFO] Running command: fastANI --query /var/lib/cwl/stg838e92ec-2ed4-4b4e-93a8-42788e975fd8/GCF_000024225.1_ASM2422v1_genomic.fna.gz --refList GCF_000024225.1_ASM2422v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000024225.1_ASM2422v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:22:22,666] [INFO] Task succeeded: fastANI
[2024-01-24 12:22:22,674] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:22:22,675] [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_000024225.1	s__Lancefieldella parvula	100.0	514	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	96.26	96.26	0.94	0.94	2	conclusive
GCA_015259035.1	s__Lancefieldella sp015259035	89.1021	281	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.13	95.13	0.67	0.67	2	-
GCA_015258715.1	s__Lancefieldella sp015258715	88.9306	423	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000564995.1	s__Lancefieldella sp000564995	88.8861	422	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.37	95.06	0.93	0.85	23	-
GCA_015259105.1	s__Lancefieldella sp015259105	88.8495	352	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.21	95.21	0.86	0.86	2	-
GCA_015258605.1	s__Lancefieldella sp015258605	88.8186	280	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
GCA_015259045.1	s__Lancefieldella sp015259045	88.7221	277	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	95.43	95.43	0.88	0.88	2	-
GCA_900555335.1	s__Lancefieldella sp900555335	88.6731	300	514	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Atopobiaceae;g__Lancefieldella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:22:22,676] [INFO] GTDB search result was written to GCF_000024225.1_ASM2422v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:22:22,677] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:22:22,680] [INFO] DFAST_QC result json was written to GCF_000024225.1_ASM2422v1_genomic.fna/dqc_result.json
[2024-01-24 12:22:22,681] [INFO] DFAST_QC completed!
[2024-01-24 12:22:22,681] [INFO] Total running time: 0h0m38s