[2024-01-24 13:45:46,298] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:46,304] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:46,304] [INFO] DQC Reference Directory: /var/lib/cwl/stg0ec39696-8db7-43e8-af0b-c730983a4af3/dqc_reference
[2024-01-24 13:45:47,728] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:47,729] [INFO] Task started: Prodigal
[2024-01-24 13:45:47,729] [INFO] Running command: gunzip -c /var/lib/cwl/stg27dbdebc-3579-4589-ba1b-9bf8ca81b0dd/GCF_012396315.1_ASM1239631v1_genomic.fna.gz | prodigal -d GCF_012396315.1_ASM1239631v1_genomic.fna/cds.fna -a GCF_012396315.1_ASM1239631v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:45:54,937] [INFO] Task succeeded: Prodigal
[2024-01-24 13:45:54,938] [INFO] Task started: HMMsearch
[2024-01-24 13:45:54,938] [INFO] Running command: hmmsearch --tblout GCF_012396315.1_ASM1239631v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0ec39696-8db7-43e8-af0b-c730983a4af3/dqc_reference/reference_markers.hmm GCF_012396315.1_ASM1239631v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:45:55,253] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:45:55,254] [INFO] Found 6/6 markers.
[2024-01-24 13:45:55,277] [INFO] Query marker FASTA was written to GCF_012396315.1_ASM1239631v1_genomic.fna/markers.fasta
[2024-01-24 13:45:55,278] [INFO] Task started: Blastn
[2024-01-24 13:45:55,278] [INFO] Running command: blastn -query GCF_012396315.1_ASM1239631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec39696-8db7-43e8-af0b-c730983a4af3/dqc_reference/reference_markers.fasta -out GCF_012396315.1_ASM1239631v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:45:56,300] [INFO] Task succeeded: Blastn
[2024-01-24 13:45:56,304] [INFO] Selected 9 target genomes.
[2024-01-24 13:45:56,304] [INFO] Target genome list was writen to GCF_012396315.1_ASM1239631v1_genomic.fna/target_genomes.txt
[2024-01-24 13:45:56,311] [INFO] Task started: fastANI
[2024-01-24 13:45:56,311] [INFO] Running command: fastANI --query /var/lib/cwl/stg27dbdebc-3579-4589-ba1b-9bf8ca81b0dd/GCF_012396315.1_ASM1239631v1_genomic.fna.gz --refList GCF_012396315.1_ASM1239631v1_genomic.fna/target_genomes.txt --output GCF_012396315.1_ASM1239631v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:01,315] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:01,316] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0ec39696-8db7-43e8-af0b-c730983a4af3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:01,316] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0ec39696-8db7-43e8-af0b-c730983a4af3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:01,325] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:46:01,325] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:46:01,325] [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 mucifaciens	strain=ATCC 700355	GCA_012396315.1	57171	57171	type	True	100.0	713	716	95	inconclusive
Corynebacterium ureicelerivorans	strain=IMMIB RIV-2301	GCA_000747315.1	401472	401472	type	True	95.7074	638	716	95	inconclusive
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	85.8432	609	716	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	85.3092	598	716	95	below_threshold
Corynebacterium wankanglinii	strain=zg-913	GCA_013601005.1	2735136	2735136	type	True	85.2354	573	716	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	85.1776	581	716	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	84.8492	585	716	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	82.6866	514	716	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	82.5671	530	716	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:01,330] [INFO] DFAST Taxonomy check result was written to GCF_012396315.1_ASM1239631v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:01,331] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:01,331] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:01,331] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0ec39696-8db7-43e8-af0b-c730983a4af3/dqc_reference/checkm_data
[2024-01-24 13:46:01,332] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:01,362] [INFO] Task started: CheckM
[2024-01-24 13:46:01,362] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396315.1_ASM1239631v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396315.1_ASM1239631v1_genomic.fna/checkm_input GCF_012396315.1_ASM1239631v1_genomic.fna/checkm_result
[2024-01-24 13:46:28,552] [INFO] Task succeeded: CheckM
[2024-01-24 13:46:28,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:46:28,571] [INFO] ===== Completeness check finished =====
[2024-01-24 13:46:28,571] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:46:28,571] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396315.1_ASM1239631v1_genomic.fna/markers.fasta)
[2024-01-24 13:46:28,572] [INFO] Task started: Blastn
[2024-01-24 13:46:28,572] [INFO] Running command: blastn -query GCF_012396315.1_ASM1239631v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0ec39696-8db7-43e8-af0b-c730983a4af3/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396315.1_ASM1239631v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:30,101] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:30,104] [INFO] Selected 9 target genomes.
[2024-01-24 13:46:30,104] [INFO] Target genome list was writen to GCF_012396315.1_ASM1239631v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:46:30,110] [INFO] Task started: fastANI
[2024-01-24 13:46:30,111] [INFO] Running command: fastANI --query /var/lib/cwl/stg27dbdebc-3579-4589-ba1b-9bf8ca81b0dd/GCF_012396315.1_ASM1239631v1_genomic.fna.gz --refList GCF_012396315.1_ASM1239631v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396315.1_ASM1239631v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:46:35,171] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:35,184] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:46:35,184] [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_012396315.1	s__Corynebacterium mucifaciens	100.0	713	716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	95.74	95.74	0.89	0.89	2	conclusive
GCF_013978595.1	s__Corynebacterium haemomassiliense	85.8362	610	716	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	85.4148	593	716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCF_015351335.1	s__Corynebacterium lipophilum	85.3092	598	716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900156035.1	s__Corynebacterium afermentans	85.3083	583	716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCA_014490595.1	s__Corynebacterium sp014490595	84.8919	492	716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.54	97.13	0.94	0.90	3	-
GCF_900176865.1	s__Corynebacterium fournieri	84.8492	585	716	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	82.5824	529	716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_903645305.1	s__Corynebacterium sp001764565	81.571	485	716	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.10	98.10	0.96	0.96	2	-
--------------------------------------------------------------------------------
[2024-01-24 13:46:35,186] [INFO] GTDB search result was written to GCF_012396315.1_ASM1239631v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:46:35,186] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:46:35,189] [INFO] DFAST_QC result json was written to GCF_012396315.1_ASM1239631v1_genomic.fna/dqc_result.json
[2024-01-24 13:46:35,190] [INFO] DFAST_QC completed!
[2024-01-24 13:46:35,190] [INFO] Total running time: 0h0m49s