[2024-01-24 13:09:33,854] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:09:33,856] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:09:33,856] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c14e198-6b34-4997-8380-77e39418e933/dqc_reference
[2024-01-24 13:09:35,204] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:09:35,205] [INFO] Task started: Prodigal
[2024-01-24 13:09:35,206] [INFO] Running command: gunzip -c /var/lib/cwl/stg2b714880-5822-4b43-9168-d88e2e20b1b8/GCF_030408575.1_ASM3040857v1_genomic.fna.gz | prodigal -d GCF_030408575.1_ASM3040857v1_genomic.fna/cds.fna -a GCF_030408575.1_ASM3040857v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:09:42,797] [INFO] Task succeeded: Prodigal
[2024-01-24 13:09:42,797] [INFO] Task started: HMMsearch
[2024-01-24 13:09:42,797] [INFO] Running command: hmmsearch --tblout GCF_030408575.1_ASM3040857v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c14e198-6b34-4997-8380-77e39418e933/dqc_reference/reference_markers.hmm GCF_030408575.1_ASM3040857v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:09:43,162] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:09:43,163] [INFO] Found 6/6 markers.
[2024-01-24 13:09:43,202] [INFO] Query marker FASTA was written to GCF_030408575.1_ASM3040857v1_genomic.fna/markers.fasta
[2024-01-24 13:09:43,202] [INFO] Task started: Blastn
[2024-01-24 13:09:43,202] [INFO] Running command: blastn -query GCF_030408575.1_ASM3040857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c14e198-6b34-4997-8380-77e39418e933/dqc_reference/reference_markers.fasta -out GCF_030408575.1_ASM3040857v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:09:44,326] [INFO] Task succeeded: Blastn
[2024-01-24 13:09:44,329] [INFO] Selected 10 target genomes.
[2024-01-24 13:09:44,330] [INFO] Target genome list was writen to GCF_030408575.1_ASM3040857v1_genomic.fna/target_genomes.txt
[2024-01-24 13:09:44,335] [INFO] Task started: fastANI
[2024-01-24 13:09:44,335] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b714880-5822-4b43-9168-d88e2e20b1b8/GCF_030408575.1_ASM3040857v1_genomic.fna.gz --refList GCF_030408575.1_ASM3040857v1_genomic.fna/target_genomes.txt --output GCF_030408575.1_ASM3040857v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:09:50,660] [INFO] Task succeeded: fastANI
[2024-01-24 13:09:50,660] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c14e198-6b34-4997-8380-77e39418e933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:09:50,661] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c14e198-6b34-4997-8380-77e39418e933/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:09:50,670] [INFO] Found 10 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 13:09:50,670] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 13:09:50,671] [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
Corynebacterium timonense	strain=5401744	GCA_000312345.1	441500	441500	type	True	88.6206	698	813	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	88.533	719	813	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	84.2955	589	813	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	81.547	468	813	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	81.2054	404	813	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	80.9378	452	813	95	below_threshold
Corynebacterium bouchesdurhonense	strain=SN14	GCA_900078305.2	1720192	1720192	type	True	80.8198	429	813	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	80.5299	423	813	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	80.3225	394	813	95	below_threshold
Corynebacterium godavarianum	strain=LMG 29598	GCA_007559235.1	2054421	2054421	type	True	80.2308	416	813	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:09:50,672] [INFO] DFAST Taxonomy check result was written to GCF_030408575.1_ASM3040857v1_genomic.fna/tc_result.tsv
[2024-01-24 13:09:50,673] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:09:50,673] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:09:50,673] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c14e198-6b34-4997-8380-77e39418e933/dqc_reference/checkm_data
[2024-01-24 13:09:50,674] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:09:50,699] [INFO] Task started: CheckM
[2024-01-24 13:09:50,699] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408575.1_ASM3040857v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408575.1_ASM3040857v1_genomic.fna/checkm_input GCF_030408575.1_ASM3040857v1_genomic.fna/checkm_result
[2024-01-24 13:10:15,644] [INFO] Task succeeded: CheckM
[2024-01-24 13:10:15,645] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:10:15,658] [INFO] ===== Completeness check finished =====
[2024-01-24 13:10:15,659] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:10:15,659] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408575.1_ASM3040857v1_genomic.fna/markers.fasta)
[2024-01-24 13:10:15,659] [INFO] Task started: Blastn
[2024-01-24 13:10:15,659] [INFO] Running command: blastn -query GCF_030408575.1_ASM3040857v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c14e198-6b34-4997-8380-77e39418e933/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408575.1_ASM3040857v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:10:17,158] [INFO] Task succeeded: Blastn
[2024-01-24 13:10:17,163] [INFO] Selected 9 target genomes.
[2024-01-24 13:10:17,163] [INFO] Target genome list was writen to GCF_030408575.1_ASM3040857v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:10:17,168] [INFO] Task started: fastANI
[2024-01-24 13:10:17,168] [INFO] Running command: fastANI --query /var/lib/cwl/stg2b714880-5822-4b43-9168-d88e2e20b1b8/GCF_030408575.1_ASM3040857v1_genomic.fna.gz --refList GCF_030408575.1_ASM3040857v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408575.1_ASM3040857v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:10:22,256] [INFO] Task succeeded: fastANI
[2024-01-24 13:10:22,264] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 13:10:22,264] [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_900105305.1	s__Corynebacterium timonense	88.5419	721	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCF_900411315.1	s__Corynebacterium senegalense	84.264	587	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339505.1	s__Corynebacterium sp002339505	82.2771	510	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103625.1	s__Corynebacterium mycetoides	81.5571	467	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000577555.1	s__Corynebacterium jeddahense	81.1617	406	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	80.9322	455	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900078305.2	s__Corynebacterium bouchesdurhonense	80.849	428	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
GCF_015351335.1	s__Corynebacterium lipophilum	80.5105	425	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001807265.1	s__Corynebacterium sp001807265	80.4598	434	813	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:10:22,266] [INFO] GTDB search result was written to GCF_030408575.1_ASM3040857v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:10:22,266] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:10:22,269] [INFO] DFAST_QC result json was written to GCF_030408575.1_ASM3040857v1_genomic.fna/dqc_result.json
[2024-01-24 13:10:22,269] [INFO] DFAST_QC completed!
[2024-01-24 13:10:22,270] [INFO] Total running time: 0h0m48s