[2024-01-24 13:35:27,614] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:35:27,616] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:35:27,616] [INFO] DQC Reference Directory: /var/lib/cwl/stgf0c2faa4-2945-460c-ad99-2595b8878012/dqc_reference
[2024-01-24 13:35:28,863] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:35:28,864] [INFO] Task started: Prodigal
[2024-01-24 13:35:28,864] [INFO] Running command: gunzip -c /var/lib/cwl/stg80d62c46-5b85-48b7-9a6e-f8fab1463b4b/GCF_003182075.1_ASM318207v1_genomic.fna.gz | prodigal -d GCF_003182075.1_ASM318207v1_genomic.fna/cds.fna -a GCF_003182075.1_ASM318207v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:35:32,882] [INFO] Task succeeded: Prodigal
[2024-01-24 13:35:32,883] [INFO] Task started: HMMsearch
[2024-01-24 13:35:32,883] [INFO] Running command: hmmsearch --tblout GCF_003182075.1_ASM318207v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf0c2faa4-2945-460c-ad99-2595b8878012/dqc_reference/reference_markers.hmm GCF_003182075.1_ASM318207v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:35:33,118] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:35:33,119] [INFO] Found 6/6 markers.
[2024-01-24 13:35:33,140] [INFO] Query marker FASTA was written to GCF_003182075.1_ASM318207v1_genomic.fna/markers.fasta
[2024-01-24 13:35:33,140] [INFO] Task started: Blastn
[2024-01-24 13:35:33,141] [INFO] Running command: blastn -query GCF_003182075.1_ASM318207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c2faa4-2945-460c-ad99-2595b8878012/dqc_reference/reference_markers.fasta -out GCF_003182075.1_ASM318207v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:33,721] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:33,725] [INFO] Selected 13 target genomes.
[2024-01-24 13:35:33,725] [INFO] Target genome list was writen to GCF_003182075.1_ASM318207v1_genomic.fna/target_genomes.txt
[2024-01-24 13:35:33,797] [INFO] Task started: fastANI
[2024-01-24 13:35:33,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d62c46-5b85-48b7-9a6e-f8fab1463b4b/GCF_003182075.1_ASM318207v1_genomic.fna.gz --refList GCF_003182075.1_ASM318207v1_genomic.fna/target_genomes.txt --output GCF_003182075.1_ASM318207v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:35:38,555] [INFO] Task succeeded: fastANI
[2024-01-24 13:35:38,555] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf0c2faa4-2945-460c-ad99-2595b8878012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:35:38,556] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf0c2faa4-2945-460c-ad99-2595b8878012/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:35:38,561] [INFO] Found 4 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:35:38,561] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:35:38,561] [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
Finegoldia magna	strain=DSM 20470	GCA_003182075.1	1260	1260	suspected-type	True	100.0	643	645	95	conclusive
Finegoldia magna	strain=FDAARGOS_1593	GCA_020731325.1	1260	1260	suspected-type	True	99.9641	621	645	95	conclusive
Lagierella massiliensis	strain=Marseille-P2012	GCA_902375645.1	1689303	1689303	type	True	78.2369	56	645	95	below_threshold
Lagierella massiliensis	strain=SIT14	GCA_001407835.1	1689303	1689303	type	True	78.2369	56	645	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:35:38,565] [INFO] DFAST Taxonomy check result was written to GCF_003182075.1_ASM318207v1_genomic.fna/tc_result.tsv
[2024-01-24 13:35:38,566] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:35:38,566] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:35:38,566] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf0c2faa4-2945-460c-ad99-2595b8878012/dqc_reference/checkm_data
[2024-01-24 13:35:38,567] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:35:38,593] [INFO] Task started: CheckM
[2024-01-24 13:35:38,594] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003182075.1_ASM318207v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003182075.1_ASM318207v1_genomic.fna/checkm_input GCF_003182075.1_ASM318207v1_genomic.fna/checkm_result
[2024-01-24 13:35:57,748] [INFO] Task succeeded: CheckM
[2024-01-24 13:35:57,750] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:35:57,770] [INFO] ===== Completeness check finished =====
[2024-01-24 13:35:57,771] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:35:57,771] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003182075.1_ASM318207v1_genomic.fna/markers.fasta)
[2024-01-24 13:35:57,772] [INFO] Task started: Blastn
[2024-01-24 13:35:57,772] [INFO] Running command: blastn -query GCF_003182075.1_ASM318207v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf0c2faa4-2945-460c-ad99-2595b8878012/dqc_reference/reference_markers_gtdb.fasta -out GCF_003182075.1_ASM318207v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:35:58,560] [INFO] Task succeeded: Blastn
[2024-01-24 13:35:58,563] [INFO] Selected 6 target genomes.
[2024-01-24 13:35:58,563] [INFO] Target genome list was writen to GCF_003182075.1_ASM318207v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:35:58,594] [INFO] Task started: fastANI
[2024-01-24 13:35:58,595] [INFO] Running command: fastANI --query /var/lib/cwl/stg80d62c46-5b85-48b7-9a6e-f8fab1463b4b/GCF_003182075.1_ASM318207v1_genomic.fna.gz --refList GCF_003182075.1_ASM318207v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003182075.1_ASM318207v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:36:01,657] [INFO] Task succeeded: fastANI
[2024-01-24 13:36:01,667] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:36:01,667] [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_003182075.1	s__Finegoldia magna	100.0	643	645	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	96.40	95.72	0.86	0.79	17	conclusive
GCF_000159695.1	s__Finegoldia magna_F	93.7742	522	645	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	95.41	95.07	0.87	0.83	5	-
GCA_018371055.1	s__Finegoldia magna_I	92.7823	353	645	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900766215.1	s__Finegoldia sp900766215	92.0593	450	645	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCA_910589545.1	s__Finegoldia sp910589545	91.7478	497	645	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000010185.1	s__Finegoldia magna_H	90.9505	500	645	d__Bacteria;p__Firmicutes_A;c__Clostridia;o__Tissierellales;f__Peptoniphilaceae;g__Finegoldia	95.0	97.29	95.99	0.88	0.82	13	-
--------------------------------------------------------------------------------
[2024-01-24 13:36:01,669] [INFO] GTDB search result was written to GCF_003182075.1_ASM318207v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:36:01,670] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:36:01,674] [INFO] DFAST_QC result json was written to GCF_003182075.1_ASM318207v1_genomic.fna/dqc_result.json
[2024-01-24 13:36:01,674] [INFO] DFAST_QC completed!
[2024-01-24 13:36:01,674] [INFO] Total running time: 0h0m34s