[2024-01-25 18:08:35,605] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:08:35,607] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:08:35,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg0f0d0ae8-ff5d-4552-ab90-1b7d4aa1668e/dqc_reference
[2024-01-25 18:08:36,743] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:08:36,743] [INFO] Task started: Prodigal
[2024-01-25 18:08:36,744] [INFO] Running command: gunzip -c /var/lib/cwl/stg931a7750-a87d-4a3c-9e97-f3e65201a539/GCF_900447205.1_52184_C01_genomic.fna.gz | prodigal -d GCF_900447205.1_52184_C01_genomic.fna/cds.fna -a GCF_900447205.1_52184_C01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:08:44,332] [INFO] Task succeeded: Prodigal
[2024-01-25 18:08:44,333] [INFO] Task started: HMMsearch
[2024-01-25 18:08:44,333] [INFO] Running command: hmmsearch --tblout GCF_900447205.1_52184_C01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0f0d0ae8-ff5d-4552-ab90-1b7d4aa1668e/dqc_reference/reference_markers.hmm GCF_900447205.1_52184_C01_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:08:44,527] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:08:44,528] [INFO] Found 6/6 markers.
[2024-01-25 18:08:44,555] [INFO] Query marker FASTA was written to GCF_900447205.1_52184_C01_genomic.fna/markers.fasta
[2024-01-25 18:08:44,556] [INFO] Task started: Blastn
[2024-01-25 18:08:44,556] [INFO] Running command: blastn -query GCF_900447205.1_52184_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f0d0ae8-ff5d-4552-ab90-1b7d4aa1668e/dqc_reference/reference_markers.fasta -out GCF_900447205.1_52184_C01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:08:45,353] [INFO] Task succeeded: Blastn
[2024-01-25 18:08:45,356] [INFO] Selected 5 target genomes.
[2024-01-25 18:08:45,356] [INFO] Target genome list was writen to GCF_900447205.1_52184_C01_genomic.fna/target_genomes.txt
[2024-01-25 18:08:45,363] [INFO] Task started: fastANI
[2024-01-25 18:08:45,363] [INFO] Running command: fastANI --query /var/lib/cwl/stg931a7750-a87d-4a3c-9e97-f3e65201a539/GCF_900447205.1_52184_C01_genomic.fna.gz --refList GCF_900447205.1_52184_C01_genomic.fna/target_genomes.txt --output GCF_900447205.1_52184_C01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:08:48,554] [INFO] Task succeeded: fastANI
[2024-01-25 18:08:48,554] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0f0d0ae8-ff5d-4552-ab90-1b7d4aa1668e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:08:48,555] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0f0d0ae8-ff5d-4552-ab90-1b7d4aa1668e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:08:48,560] [INFO] Found 5 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:08:48,560] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:08:48,560] [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 pilosum	strain=NCTC11862	GCA_900447205.1	35756	35756	type	True	100.0	862	863	95	conclusive
Corynebacterium pilosum	strain=DSM 20521	GCA_000373805.1	35756	35756	type	True	99.9538	822	863	95	conclusive
Corynebacterium pilosum	strain=CIP103422	GCA_001044155.1	35756	35756	type	True	99.9409	838	863	95	conclusive
Corynebacterium cystitidis	strain=NCTC11863	GCA_900187295.1	35757	35757	type	True	80.6617	514	863	95	below_threshold
Corynebacterium cystitidis	strain=DSM 20524	GCA_900111265.1	35757	35757	type	True	80.5479	509	863	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:08:48,561] [INFO] DFAST Taxonomy check result was written to GCF_900447205.1_52184_C01_genomic.fna/tc_result.tsv
[2024-01-25 18:08:48,562] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:08:48,562] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:08:48,562] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0f0d0ae8-ff5d-4552-ab90-1b7d4aa1668e/dqc_reference/checkm_data
[2024-01-25 18:08:48,563] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:08:48,589] [INFO] Task started: CheckM
[2024-01-25 18:08:48,589] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900447205.1_52184_C01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900447205.1_52184_C01_genomic.fna/checkm_input GCF_900447205.1_52184_C01_genomic.fna/checkm_result
[2024-01-25 18:09:13,593] [INFO] Task succeeded: CheckM
[2024-01-25 18:09:13,594] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:09:13,608] [INFO] ===== Completeness check finished =====
[2024-01-25 18:09:13,608] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:09:13,609] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900447205.1_52184_C01_genomic.fna/markers.fasta)
[2024-01-25 18:09:13,609] [INFO] Task started: Blastn
[2024-01-25 18:09:13,609] [INFO] Running command: blastn -query GCF_900447205.1_52184_C01_genomic.fna/markers.fasta -db /var/lib/cwl/stg0f0d0ae8-ff5d-4552-ab90-1b7d4aa1668e/dqc_reference/reference_markers_gtdb.fasta -out GCF_900447205.1_52184_C01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:09:14,761] [INFO] Task succeeded: Blastn
[2024-01-25 18:09:14,764] [INFO] Selected 15 target genomes.
[2024-01-25 18:09:14,764] [INFO] Target genome list was writen to GCF_900447205.1_52184_C01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:09:14,770] [INFO] Task started: fastANI
[2024-01-25 18:09:14,770] [INFO] Running command: fastANI --query /var/lib/cwl/stg931a7750-a87d-4a3c-9e97-f3e65201a539/GCF_900447205.1_52184_C01_genomic.fna.gz --refList GCF_900447205.1_52184_C01_genomic.fna/target_genomes_gtdb.txt --output GCF_900447205.1_52184_C01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:09:22,150] [INFO] Task succeeded: fastANI
[2024-01-25 18:09:22,160] [INFO] Found 15 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:09:22,160] [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_000373805.1	s__Corynebacterium pilosum	99.9538	822	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.98	99.96	0.99	0.99	3	conclusive
GCF_900187295.1	s__Corynebacterium cystitidis	80.696	516	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000739455.1	s__Corynebacterium imitans	78.7368	263	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000379425.1	s__Corynebacterium lubricantis	78.7008	325	863	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	78.6894	253	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007641235.1	s__Corynebacterium sanguinis	78.5699	248	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	-
GCF_903645305.1	s__Corynebacterium sp001764565	78.4399	233	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
GCF_900176865.1	s__Corynebacterium fournieri	78.4351	231	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014490555.1	s__Corynebacterium sp014490555	78.4303	242	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_900105505.1	s__Corynebacterium coyleae	78.4022	223	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	-
GCF_001807265.1	s__Corynebacterium sp001807265	78.3952	248	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_900105305.1	s__Corynebacterium timonense	78.2584	242	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.93	99.93	0.99	0.99	2	-
GCA_900156035.1	s__Corynebacterium afermentans	78.0986	238	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCA_002339505.1	s__Corynebacterium sp002339505	78.0257	230	863	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	78.015	230	863	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	-
--------------------------------------------------------------------------------
[2024-01-25 18:09:22,161] [INFO] GTDB search result was written to GCF_900447205.1_52184_C01_genomic.fna/result_gtdb.tsv
[2024-01-25 18:09:22,162] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:09:22,165] [INFO] DFAST_QC result json was written to GCF_900447205.1_52184_C01_genomic.fna/dqc_result.json
[2024-01-25 18:09:22,165] [INFO] DFAST_QC completed!
[2024-01-25 18:09:22,165] [INFO] Total running time: 0h0m47s