[2024-01-25 18:08:36,364] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:36,366] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:36,366] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4b326ff-3ada-4638-ba7f-075f64602922/dqc_reference
[2024-01-25 18:08:37,495] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:37,498] [INFO] Task started: Prodigal
[2024-01-25 18:08:37,498] [INFO] Running command: gunzip -c /var/lib/cwl/stg8eb88ca5-7e17-40cc-a1f3-22bca8f62da0/GCF_030408655.1_ASM3040865v1_genomic.fna.gz | prodigal -d GCF_030408655.1_ASM3040865v1_genomic.fna/cds.fna -a GCF_030408655.1_ASM3040865v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:45,990] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:45,991] [INFO] Task started: HMMsearch
[2024-01-25 18:08:45,991] [INFO] Running command: hmmsearch --tblout GCF_030408655.1_ASM3040865v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4b326ff-3ada-4638-ba7f-075f64602922/dqc_reference/reference_markers.hmm GCF_030408655.1_ASM3040865v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:46,202] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:46,204] [INFO] Found 6/6 markers.
[2024-01-25 18:08:46,229] [INFO] Query marker FASTA was written to GCF_030408655.1_ASM3040865v1_genomic.fna/markers.fasta
[2024-01-25 18:08:46,229] [INFO] Task started: Blastn
[2024-01-25 18:08:46,229] [INFO] Running command: blastn -query GCF_030408655.1_ASM3040865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4b326ff-3ada-4638-ba7f-075f64602922/dqc_reference/reference_markers.fasta -out GCF_030408655.1_ASM3040865v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:46,925] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:46,928] [INFO] Selected 6 target genomes.
[2024-01-25 18:08:46,928] [INFO] Target genome list was writen to GCF_030408655.1_ASM3040865v1_genomic.fna/target_genomes.txt
[2024-01-25 18:08:46,930] [INFO] Task started: fastANI
[2024-01-25 18:08:46,930] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb88ca5-7e17-40cc-a1f3-22bca8f62da0/GCF_030408655.1_ASM3040865v1_genomic.fna.gz --refList GCF_030408655.1_ASM3040865v1_genomic.fna/target_genomes.txt --output GCF_030408655.1_ASM3040865v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:50,574] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:50,574] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4b326ff-3ada-4638-ba7f-075f64602922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:50,574] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4b326ff-3ada-4638-ba7f-075f64602922/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:50,580] [INFO] Found 5 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:08:50,580] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:50,580] [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 cystitidis	strain=NCTC11863	GCA_900187295.1	35757	35757	type	True	99.9963	1001	1003	95	conclusive
Corynebacterium cystitidis	strain=DSM 20524	GCA_900111265.1	35757	35757	type	True	99.9491	960	1003	95	conclusive
Corynebacterium pilosum	strain=NCTC11862	GCA_900447205.1	35756	35756	type	True	80.7029	514	1003	95	below_threshold
Corynebacterium pilosum	strain=DSM 20521	GCA_000373805.1	35756	35756	type	True	80.6675	495	1003	95	below_threshold
Corynebacterium pilosum	strain=CIP103422	GCA_001044155.1	35756	35756	type	True	80.6242	497	1003	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:50,582] [INFO] DFAST Taxonomy check result was written to GCF_030408655.1_ASM3040865v1_genomic.fna/tc_result.tsv
[2024-01-25 18:08:50,583] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:50,583] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:50,583] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4b326ff-3ada-4638-ba7f-075f64602922/dqc_reference/checkm_data
[2024-01-25 18:08:50,584] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:50,616] [INFO] Task started: CheckM
[2024-01-25 18:08:50,616] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408655.1_ASM3040865v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408655.1_ASM3040865v1_genomic.fna/checkm_input GCF_030408655.1_ASM3040865v1_genomic.fna/checkm_result
[2024-01-25 18:09:18,038] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:18,039] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:18,054] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:18,055] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:18,055] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408655.1_ASM3040865v1_genomic.fna/markers.fasta)
[2024-01-25 18:09:18,055] [INFO] Task started: Blastn
[2024-01-25 18:09:18,055] [INFO] Running command: blastn -query GCF_030408655.1_ASM3040865v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4b326ff-3ada-4638-ba7f-075f64602922/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408655.1_ASM3040865v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:19,053] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:19,056] [INFO] Selected 16 target genomes.
[2024-01-25 18:09:19,057] [INFO] Target genome list was writen to GCF_030408655.1_ASM3040865v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:19,076] [INFO] Task started: fastANI
[2024-01-25 18:09:19,077] [INFO] Running command: fastANI --query /var/lib/cwl/stg8eb88ca5-7e17-40cc-a1f3-22bca8f62da0/GCF_030408655.1_ASM3040865v1_genomic.fna.gz --refList GCF_030408655.1_ASM3040865v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408655.1_ASM3040865v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:26,104] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:26,113] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:26,113] [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_900187295.1	s__Corynebacterium cystitidis	99.9964	1001	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	conclusive
GCF_000373805.1	s__Corynebacterium pilosum	80.663	495	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.96	0.99	0.99	3	-
GCF_000379425.1	s__Corynebacterium lubricantis	78.2972	208	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000980815.1	s__Corynebacterium camporealensis	78.2929	114	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.96	99.96	1.00	1.00	2	-
GCF_014490555.1	s__Corynebacterium sp014490555	77.9126	144	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_900103625.1	s__Corynebacterium mycetoides	77.8947	147	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900105505.1	s__Corynebacterium coyleae	77.8761	154	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	77.6445	165	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000159635.1	s__Corynebacterium lipophiloflavum	77.5193	133	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396315.1	s__Corynebacterium mucifaciens	77.496	131	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
GCF_003693265.1	s__Corynebacterium gottingense	77.4573	134	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
GCF_015351335.1	s__Corynebacterium lipophilum	77.4189	155	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006334925.1	s__Corynebacterium tapiri	77.3687	116	1003	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	77.368	160	1003	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:26,115] [INFO] GTDB search result was written to GCF_030408655.1_ASM3040865v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:26,116] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:26,118] [INFO] DFAST_QC result json was written to GCF_030408655.1_ASM3040865v1_genomic.fna/dqc_result.json
[2024-01-25 18:09:26,119] [INFO] DFAST_QC completed!
[2024-01-25 18:09:26,119] [INFO] Total running time: 0h0m50s