[2024-01-24 12:52:25,604] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:52:25,606] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:52:25,607] [INFO] DQC Reference Directory: /var/lib/cwl/stg089e21c9-3530-44f1-b88a-375f3331e6d9/dqc_reference
[2024-01-24 12:52:26,907] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:52:26,909] [INFO] Task started: Prodigal
[2024-01-24 12:52:26,910] [INFO] Running command: gunzip -c /var/lib/cwl/stg1d070a81-3ee9-4bf2-8e86-b9ca5811491d/GCF_030408795.1_ASM3040879v1_genomic.fna.gz | prodigal -d GCF_030408795.1_ASM3040879v1_genomic.fna/cds.fna -a GCF_030408795.1_ASM3040879v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:52:36,238] [INFO] Task succeeded: Prodigal
[2024-01-24 12:52:36,239] [INFO] Task started: HMMsearch
[2024-01-24 12:52:36,239] [INFO] Running command: hmmsearch --tblout GCF_030408795.1_ASM3040879v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg089e21c9-3530-44f1-b88a-375f3331e6d9/dqc_reference/reference_markers.hmm GCF_030408795.1_ASM3040879v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:52:36,493] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:52:36,495] [INFO] Found 6/6 markers.
[2024-01-24 12:52:36,521] [INFO] Query marker FASTA was written to GCF_030408795.1_ASM3040879v1_genomic.fna/markers.fasta
[2024-01-24 12:52:36,521] [INFO] Task started: Blastn
[2024-01-24 12:52:36,522] [INFO] Running command: blastn -query GCF_030408795.1_ASM3040879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg089e21c9-3530-44f1-b88a-375f3331e6d9/dqc_reference/reference_markers.fasta -out GCF_030408795.1_ASM3040879v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:52:37,688] [INFO] Task succeeded: Blastn
[2024-01-24 12:52:37,692] [INFO] Selected 11 target genomes.
[2024-01-24 12:52:37,693] [INFO] Target genome list was writen to GCF_030408795.1_ASM3040879v1_genomic.fna/target_genomes.txt
[2024-01-24 12:52:37,704] [INFO] Task started: fastANI
[2024-01-24 12:52:37,704] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d070a81-3ee9-4bf2-8e86-b9ca5811491d/GCF_030408795.1_ASM3040879v1_genomic.fna.gz --refList GCF_030408795.1_ASM3040879v1_genomic.fna/target_genomes.txt --output GCF_030408795.1_ASM3040879v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:52:44,028] [INFO] Task succeeded: fastANI
[2024-01-24 12:52:44,029] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg089e21c9-3530-44f1-b88a-375f3331e6d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:52:44,029] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg089e21c9-3530-44f1-b88a-375f3331e6d9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:52:44,044] [INFO] Found 11 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:52:44,044] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:52:44,044] [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 xerosis	strain=NBRC 16721	GCA_001552415.1	1725	1725	suspected-type	True	87.7574	780	1032	95	below_threshold
Corynebacterium freneyi	strain=DSM 44506	GCA_017876455.1	134034	134034	type	True	87.6395	788	1032	95	below_threshold
Corynebacterium freneyi	strain=FDAARGOS 1426	GCA_019047805.1	134034	134034	type	True	87.5551	802	1032	95	below_threshold
Corynebacterium sphenisci	strain=DSM 44792	GCA_001941505.1	191493	191493	type	True	80.3417	501	1032	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	79.4834	319	1032	95	below_threshold
Corynebacterium lactis	strain=RW2-5	GCA_001274895.1	1231000	1231000	type	True	79.3398	303	1032	95	below_threshold
Corynebacterium sputi	strain=DSM 45148	GCA_000427865.1	489915	489915	type	True	78.7358	278	1032	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	78.5102	233	1032	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	78.371	231	1032	95	below_threshold
Corynebacterium mastitidis	strain=DSM 44356	GCA_000375365.1	161890	161890	type	True	78.0055	264	1032	95	below_threshold
Rhodococcus maanshanensis	strain=DSM 44675	GCA_900109405.1	183556	183556	type	True	77.351	259	1032	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:52:44,047] [INFO] DFAST Taxonomy check result was written to GCF_030408795.1_ASM3040879v1_genomic.fna/tc_result.tsv
[2024-01-24 12:52:44,048] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:52:44,048] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:52:44,060] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg089e21c9-3530-44f1-b88a-375f3331e6d9/dqc_reference/checkm_data
[2024-01-24 12:52:44,062] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:52:44,097] [INFO] Task started: CheckM
[2024-01-24 12:52:44,097] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408795.1_ASM3040879v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408795.1_ASM3040879v1_genomic.fna/checkm_input GCF_030408795.1_ASM3040879v1_genomic.fna/checkm_result
[2024-01-24 12:53:20,322] [INFO] Task succeeded: CheckM
[2024-01-24 12:53:20,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.37%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:53:20,434] [INFO] ===== Completeness check finished =====
[2024-01-24 12:53:20,435] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:53:20,435] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408795.1_ASM3040879v1_genomic.fna/markers.fasta)
[2024-01-24 12:53:20,436] [INFO] Task started: Blastn
[2024-01-24 12:53:20,436] [INFO] Running command: blastn -query GCF_030408795.1_ASM3040879v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg089e21c9-3530-44f1-b88a-375f3331e6d9/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408795.1_ASM3040879v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:53:22,241] [INFO] Task succeeded: Blastn
[2024-01-24 12:53:22,244] [INFO] Selected 7 target genomes.
[2024-01-24 12:53:22,244] [INFO] Target genome list was writen to GCF_030408795.1_ASM3040879v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:53:22,270] [INFO] Task started: fastANI
[2024-01-24 12:53:22,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg1d070a81-3ee9-4bf2-8e86-b9ca5811491d/GCF_030408795.1_ASM3040879v1_genomic.fna.gz --refList GCF_030408795.1_ASM3040879v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408795.1_ASM3040879v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:53:27,092] [INFO] Task succeeded: fastANI
[2024-01-24 12:53:27,104] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:53:27,104] [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_001056295.1	s__Corynebacterium halotolerans_A	98.1864	958	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_012837295.1	s__Corynebacterium sp012837295	88.2734	600	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552415.1	s__Corynebacterium xerosis	87.7606	780	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.07	95.54	0.95	0.90	8	-
GCF_017876455.1	s__Corynebacterium freneyi	87.6077	790	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.50	96.48	0.94	0.86	4	-
GCA_012838715.1	s__Corynebacterium sp012838715	84.468	439	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941505.1	s__Corynebacterium sphenisci	80.36	497	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019209905.1	s__Corynebacterium sp019209905	79.0112	244	1032	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:53:27,106] [INFO] GTDB search result was written to GCF_030408795.1_ASM3040879v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:53:27,106] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:53:27,109] [INFO] DFAST_QC result json was written to GCF_030408795.1_ASM3040879v1_genomic.fna/dqc_result.json
[2024-01-24 12:53:27,109] [INFO] DFAST_QC completed!
[2024-01-24 12:53:27,109] [INFO] Total running time: 0h1m2s