[2024-01-24 13:27:46,474] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:27:46,476] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:27:46,477] [INFO] DQC Reference Directory: /var/lib/cwl/stga7fca2fc-b096-4de1-84ae-55cd355bbac9/dqc_reference
[2024-01-24 13:27:47,926] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:27:47,928] [INFO] Task started: Prodigal
[2024-01-24 13:27:47,928] [INFO] Running command: gunzip -c /var/lib/cwl/stg0798b719-1ea2-46ce-a994-8c7307e4cf17/GCF_008831045.1_ASM883104v1_genomic.fna.gz | prodigal -d GCF_008831045.1_ASM883104v1_genomic.fna/cds.fna -a GCF_008831045.1_ASM883104v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:27:59,505] [INFO] Task succeeded: Prodigal
[2024-01-24 13:27:59,506] [INFO] Task started: HMMsearch
[2024-01-24 13:27:59,506] [INFO] Running command: hmmsearch --tblout GCF_008831045.1_ASM883104v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stga7fca2fc-b096-4de1-84ae-55cd355bbac9/dqc_reference/reference_markers.hmm GCF_008831045.1_ASM883104v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:27:59,802] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:27:59,803] [INFO] Found 6/6 markers.
[2024-01-24 13:27:59,831] [INFO] Query marker FASTA was written to GCF_008831045.1_ASM883104v1_genomic.fna/markers.fasta
[2024-01-24 13:27:59,831] [INFO] Task started: Blastn
[2024-01-24 13:27:59,832] [INFO] Running command: blastn -query GCF_008831045.1_ASM883104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7fca2fc-b096-4de1-84ae-55cd355bbac9/dqc_reference/reference_markers.fasta -out GCF_008831045.1_ASM883104v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:00,606] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:00,610] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:00,610] [INFO] Target genome list was writen to GCF_008831045.1_ASM883104v1_genomic.fna/target_genomes.txt
[2024-01-24 13:28:00,621] [INFO] Task started: fastANI
[2024-01-24 13:28:00,621] [INFO] Running command: fastANI --query /var/lib/cwl/stg0798b719-1ea2-46ce-a994-8c7307e4cf17/GCF_008831045.1_ASM883104v1_genomic.fna.gz --refList GCF_008831045.1_ASM883104v1_genomic.fna/target_genomes.txt --output GCF_008831045.1_ASM883104v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:28:07,052] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:07,052] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stga7fca2fc-b096-4de1-84ae-55cd355bbac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:28:07,053] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stga7fca2fc-b096-4de1-84ae-55cd355bbac9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:28:07,061] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:28:07,062] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:28:07,062] [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 muris	strain=DSM 29508	GCA_008831045.1	1796610	1796610	type	True	100.0	874	876	95	conclusive
Adlercreutzia muris	strain=DSM 29508	GCA_024623245.1	1796610	1796610	type	True	99.9974	865	876	95	conclusive
Adlercreutzia caecimuris	strain=DSM 21839	GCA_024623275.1	671266	671266	type	True	90.8813	646	876	95	below_threshold
Adlercreutzia caecimuris	strain=B7	GCA_000403355.2	671266	671266	type	True	90.7653	645	876	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_000422625.1	580026	580026	type	True	89.1651	588	876	95	below_threshold
Adlercreutzia mucosicola	strain=DSM 19490	GCA_024623255.1	580026	580026	type	True	89.0622	566	876	95	below_threshold
Adlercreutzia hattorii	strain=8CFCBH1	GCA_011405655.1	2707299	2707299	type	True	84.5788	552	876	95	below_threshold
Slackia exigua	strain=NCTC12994	GCA_900450505.1	84109	84109	type	True	77.4706	112	876	95	below_threshold
Slackia exigua	strain=ATCC 700122	GCA_000162875.1	84109	84109	type	True	77.4514	109	876	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:28:07,063] [INFO] DFAST Taxonomy check result was written to GCF_008831045.1_ASM883104v1_genomic.fna/tc_result.tsv
[2024-01-24 13:28:07,064] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:28:07,064] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:28:07,064] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stga7fca2fc-b096-4de1-84ae-55cd355bbac9/dqc_reference/checkm_data
[2024-01-24 13:28:07,066] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:28:07,096] [INFO] Task started: CheckM
[2024-01-24 13:28:07,096] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_008831045.1_ASM883104v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_008831045.1_ASM883104v1_genomic.fna/checkm_input GCF_008831045.1_ASM883104v1_genomic.fna/checkm_result
[2024-01-24 13:28:41,741] [INFO] Task succeeded: CheckM
[2024-01-24 13:28:41,742] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:28:41,764] [INFO] ===== Completeness check finished =====
[2024-01-24 13:28:41,765] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:28:41,766] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_008831045.1_ASM883104v1_genomic.fna/markers.fasta)
[2024-01-24 13:28:41,767] [INFO] Task started: Blastn
[2024-01-24 13:28:41,767] [INFO] Running command: blastn -query GCF_008831045.1_ASM883104v1_genomic.fna/markers.fasta -db /var/lib/cwl/stga7fca2fc-b096-4de1-84ae-55cd355bbac9/dqc_reference/reference_markers_gtdb.fasta -out GCF_008831045.1_ASM883104v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:28:42,937] [INFO] Task succeeded: Blastn
[2024-01-24 13:28:42,941] [INFO] Selected 10 target genomes.
[2024-01-24 13:28:42,941] [INFO] Target genome list was writen to GCF_008831045.1_ASM883104v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:28:42,953] [INFO] Task started: fastANI
[2024-01-24 13:28:42,954] [INFO] Running command: fastANI --query /var/lib/cwl/stg0798b719-1ea2-46ce-a994-8c7307e4cf17/GCF_008831045.1_ASM883104v1_genomic.fna.gz --refList GCF_008831045.1_ASM883104v1_genomic.fna/target_genomes_gtdb.txt --output GCF_008831045.1_ASM883104v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:28:48,722] [INFO] Task succeeded: fastANI
[2024-01-24 13:28:48,736] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:28:48,736] [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_008831045.1	s__Adlercreutzia muris	100.0	874	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.80	97.69	0.87	0.84	7	conclusive
GCF_000403355.2	s__Adlercreutzia caecimuris	90.7603	645	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.41	97.35	0.86	0.85	5	-
GCF_000422625.1	s__Adlercreutzia mucosicola	89.1651	588	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.91	97.91	0.87	0.87	2	-
GCF_011405655.1	s__Adlercreutzia celatus_A	84.5683	553	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	96.32	95.52	0.87	0.80	16	-
GCF_000478885.1	s__Adlercreutzia equolifaciens	84.0635	577	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	97.05	95.56	0.84	0.79	7	-
GCA_910589165.1	s__Adlercreutzia sp910589165	83.536	518	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Adlercreutzia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902386925.1	s__Arabia massiliensis	80.0097	340	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Arabia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_905236045.1	s__Denitrobacterium sp905236045	77.4529	121	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Denitrobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017533165.1	s__RGIG3135 sp017533165	77.3894	91	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__RGIG3135	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009782605.1	s__Raoultibacter sp009782605	77.2053	125	876	d__Bacteria;p__Actinobacteriota;c__Coriobacteriia;o__Coriobacteriales;f__Eggerthellaceae;g__Raoultibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:28:48,739] [INFO] GTDB search result was written to GCF_008831045.1_ASM883104v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:28:48,740] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:28:48,744] [INFO] DFAST_QC result json was written to GCF_008831045.1_ASM883104v1_genomic.fna/dqc_result.json
[2024-01-24 13:28:48,744] [INFO] DFAST_QC completed!
[2024-01-24 13:28:48,744] [INFO] Total running time: 0h1m2s