[2024-01-24 10:47:06,548] [INFO] DFAST_QC pipeline started.
[2024-01-24 10:47:06,552] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 10:47:06,552] [INFO] DQC Reference Directory: /var/lib/cwl/stg2119c4b5-debd-4b28-ae7f-776d829fde86/dqc_reference
[2024-01-24 10:47:12,104] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 10:47:12,105] [INFO] Task started: Prodigal
[2024-01-24 10:47:12,105] [INFO] Running command: gunzip -c /var/lib/cwl/stgc32e4a87-8c8a-45b4-b689-e02684167f2b/GCF_030408635.1_ASM3040863v1_genomic.fna.gz | prodigal -d GCF_030408635.1_ASM3040863v1_genomic.fna/cds.fna -a GCF_030408635.1_ASM3040863v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 10:47:20,564] [INFO] Task succeeded: Prodigal
[2024-01-24 10:47:20,565] [INFO] Task started: HMMsearch
[2024-01-24 10:47:20,565] [INFO] Running command: hmmsearch --tblout GCF_030408635.1_ASM3040863v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2119c4b5-debd-4b28-ae7f-776d829fde86/dqc_reference/reference_markers.hmm GCF_030408635.1_ASM3040863v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 10:47:20,769] [INFO] Task succeeded: HMMsearch
[2024-01-24 10:47:20,771] [INFO] Found 6/6 markers.
[2024-01-24 10:47:20,795] [INFO] Query marker FASTA was written to GCF_030408635.1_ASM3040863v1_genomic.fna/markers.fasta
[2024-01-24 10:47:20,795] [INFO] Task started: Blastn
[2024-01-24 10:47:20,795] [INFO] Running command: blastn -query GCF_030408635.1_ASM3040863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2119c4b5-debd-4b28-ae7f-776d829fde86/dqc_reference/reference_markers.fasta -out GCF_030408635.1_ASM3040863v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:21,828] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:21,831] [INFO] Selected 7 target genomes.
[2024-01-24 10:47:21,831] [INFO] Target genome list was writen to GCF_030408635.1_ASM3040863v1_genomic.fna/target_genomes.txt
[2024-01-24 10:47:21,836] [INFO] Task started: fastANI
[2024-01-24 10:47:21,836] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32e4a87-8c8a-45b4-b689-e02684167f2b/GCF_030408635.1_ASM3040863v1_genomic.fna.gz --refList GCF_030408635.1_ASM3040863v1_genomic.fna/target_genomes.txt --output GCF_030408635.1_ASM3040863v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 10:47:26,292] [INFO] Task succeeded: fastANI
[2024-01-24 10:47:26,293] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2119c4b5-debd-4b28-ae7f-776d829fde86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 10:47:26,293] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2119c4b5-debd-4b28-ae7f-776d829fde86/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 10:47:26,300] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 10:47:26,300] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 10:47:26,300] [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 coyleae	strain=FDAARGOS 1425	GCA_019048165.1	53374	53374	type	True	99.9969	835	836	95	conclusive
Corynebacterium coyleae	strain=DSM 44184	GCA_900105505.1	53374	53374	type	True	99.9966	836	836	95	conclusive
Corynebacterium lujinxingii	strain=zg-917	GCA_014267325.1	2763010	2763010	type	True	83.818	563	836	95	below_threshold
Corynebacterium lujinxingii	strain=zg-917	GCA_014490555.1	2763010	2763010	type	True	83.7282	595	836	95	below_threshold
Corynebacterium haemomassiliense	strain=Marseille-Q3615	GCA_013978595.1	2754726	2754726	type	True	82.9699	563	836	95	below_threshold
Corynebacterium ihumii	strain=GD7	GCA_000403725.2	1232427	1232427	type	True	82.335	517	836	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	82.2778	535	836	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 10:47:26,306] [INFO] DFAST Taxonomy check result was written to GCF_030408635.1_ASM3040863v1_genomic.fna/tc_result.tsv
[2024-01-24 10:47:26,306] [INFO] ===== Taxonomy check completed =====
[2024-01-24 10:47:26,307] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 10:47:26,307] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2119c4b5-debd-4b28-ae7f-776d829fde86/dqc_reference/checkm_data
[2024-01-24 10:47:26,308] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 10:47:26,333] [INFO] Task started: CheckM
[2024-01-24 10:47:26,334] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408635.1_ASM3040863v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408635.1_ASM3040863v1_genomic.fna/checkm_input GCF_030408635.1_ASM3040863v1_genomic.fna/checkm_result
[2024-01-24 10:47:56,024] [INFO] Task succeeded: CheckM
[2024-01-24 10:47:56,025] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 10:47:56,043] [INFO] ===== Completeness check finished =====
[2024-01-24 10:47:56,044] [INFO] ===== Start GTDB Search =====
[2024-01-24 10:47:56,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408635.1_ASM3040863v1_genomic.fna/markers.fasta)
[2024-01-24 10:47:56,045] [INFO] Task started: Blastn
[2024-01-24 10:47:56,045] [INFO] Running command: blastn -query GCF_030408635.1_ASM3040863v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2119c4b5-debd-4b28-ae7f-776d829fde86/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408635.1_ASM3040863v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 10:47:57,577] [INFO] Task succeeded: Blastn
[2024-01-24 10:47:57,580] [INFO] Selected 7 target genomes.
[2024-01-24 10:47:57,580] [INFO] Target genome list was writen to GCF_030408635.1_ASM3040863v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 10:47:57,588] [INFO] Task started: fastANI
[2024-01-24 10:47:57,588] [INFO] Running command: fastANI --query /var/lib/cwl/stgc32e4a87-8c8a-45b4-b689-e02684167f2b/GCF_030408635.1_ASM3040863v1_genomic.fna.gz --refList GCF_030408635.1_ASM3040863v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408635.1_ASM3040863v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 10:48:02,338] [INFO] Task succeeded: fastANI
[2024-01-24 10:48:02,346] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 10:48:02,347] [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_900105505.1	s__Corynebacterium coyleae	99.9966	836	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.88	97.68	0.93	0.91	16	conclusive
GCF_014490555.1	s__Corynebacterium sp014490555	83.7529	595	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	0.99	3	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	82.9821	564	836	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	82.6834	544	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.96	97.96	0.92	0.92	2	-
GCA_900156035.1	s__Corynebacterium afermentans	82.3983	511	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
GCF_015351335.1	s__Corynebacterium lipophilum	82.2991	533	836	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900176865.1	s__Corynebacterium fournieri	82.0446	514	836	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 10:48:02,348] [INFO] GTDB search result was written to GCF_030408635.1_ASM3040863v1_genomic.fna/result_gtdb.tsv
[2024-01-24 10:48:02,350] [INFO] ===== GTDB Search completed =====
[2024-01-24 10:48:02,352] [INFO] DFAST_QC result json was written to GCF_030408635.1_ASM3040863v1_genomic.fna/dqc_result.json
[2024-01-24 10:48:02,353] [INFO] DFAST_QC completed!
[2024-01-24 10:48:02,353] [INFO] Total running time: 0h0m56s