[2024-01-24 13:42:57,193] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:42:57,195] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:42:57,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg64bc1dfd-5db2-451d-97ef-a82c1324f5bf/dqc_reference
[2024-01-24 13:42:58,487] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:42:58,488] [INFO] Task started: Prodigal
[2024-01-24 13:42:58,488] [INFO] Running command: gunzip -c /var/lib/cwl/stg0ccb726c-5bbf-4ca7-b6ec-3f15a5e93943/GCF_007641235.1_ASM764123v1_genomic.fna.gz | prodigal -d GCF_007641235.1_ASM764123v1_genomic.fna/cds.fna -a GCF_007641235.1_ASM764123v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:43:05,924] [INFO] Task succeeded: Prodigal
[2024-01-24 13:43:05,925] [INFO] Task started: HMMsearch
[2024-01-24 13:43:05,925] [INFO] Running command: hmmsearch --tblout GCF_007641235.1_ASM764123v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg64bc1dfd-5db2-451d-97ef-a82c1324f5bf/dqc_reference/reference_markers.hmm GCF_007641235.1_ASM764123v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:43:06,158] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:43:06,160] [INFO] Found 6/6 markers.
[2024-01-24 13:43:06,186] [INFO] Query marker FASTA was written to GCF_007641235.1_ASM764123v1_genomic.fna/markers.fasta
[2024-01-24 13:43:06,187] [INFO] Task started: Blastn
[2024-01-24 13:43:06,187] [INFO] Running command: blastn -query GCF_007641235.1_ASM764123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64bc1dfd-5db2-451d-97ef-a82c1324f5bf/dqc_reference/reference_markers.fasta -out GCF_007641235.1_ASM764123v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:07,165] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:07,169] [INFO] Selected 9 target genomes.
[2024-01-24 13:43:07,169] [INFO] Target genome list was writen to GCF_007641235.1_ASM764123v1_genomic.fna/target_genomes.txt
[2024-01-24 13:43:07,175] [INFO] Task started: fastANI
[2024-01-24 13:43:07,176] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ccb726c-5bbf-4ca7-b6ec-3f15a5e93943/GCF_007641235.1_ASM764123v1_genomic.fna.gz --refList GCF_007641235.1_ASM764123v1_genomic.fna/target_genomes.txt --output GCF_007641235.1_ASM764123v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:43:12,155] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:12,156] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg64bc1dfd-5db2-451d-97ef-a82c1324f5bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:43:12,157] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg64bc1dfd-5db2-451d-97ef-a82c1324f5bf/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:43:12,172] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:43:12,172] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:43:12,173] [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 sanguinis	strain=CCUG 58655	GCA_007641235.1	2594913	2594913	type	True	100.0	786	787	95	conclusive
Corynebacterium lipophiloflavum	strain=DSM 44291	GCA_000159635.1	161889	161889	type	True	92.407	665	787	95	below_threshold
Corynebacterium mycetoides	strain=DSM 20632	GCA_900103625.1	38302	38302	type	True	83.9307	584	787	95	below_threshold
Corynebacterium qintianiae	strain=MC1420	GCA_011038645.2	2709392	2709392	type	True	83.5418	551	787	95	below_threshold
Corynebacterium liangguodongii	strain=2184	GCA_003070865.1	2079535	2079535	type	True	82.1694	502	787	95	below_threshold
Corynebacterium senegalense	strain=Marseille-P4329	GCA_900411315.1	2080750	2080750	type	True	81.8673	526	787	95	below_threshold
Corynebacterium jeddahense	strain=JCB	GCA_000577555.1	1414719	1414719	type	True	81.0943	380	787	95	below_threshold
Corynebacterium timonense	strain=DSM 45434	GCA_900105305.1	441500	441500	type	True	80.965	487	787	95	below_threshold
Corynebacterium afermentans subsp. lipophilum	strain=CCUG 32105	GCA_015351335.1	144184	38286	type	True	80.3596	388	787	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:43:12,175] [INFO] DFAST Taxonomy check result was written to GCF_007641235.1_ASM764123v1_genomic.fna/tc_result.tsv
[2024-01-24 13:43:12,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:43:12,176] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:43:12,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg64bc1dfd-5db2-451d-97ef-a82c1324f5bf/dqc_reference/checkm_data
[2024-01-24 13:43:12,178] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:43:12,207] [INFO] Task started: CheckM
[2024-01-24 13:43:12,207] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_007641235.1_ASM764123v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_007641235.1_ASM764123v1_genomic.fna/checkm_input GCF_007641235.1_ASM764123v1_genomic.fna/checkm_result
[2024-01-24 13:43:37,846] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:37,847] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:43:37,864] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:37,864] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:37,865] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_007641235.1_ASM764123v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:37,865] [INFO] Task started: Blastn
[2024-01-24 13:43:37,865] [INFO] Running command: blastn -query GCF_007641235.1_ASM764123v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg64bc1dfd-5db2-451d-97ef-a82c1324f5bf/dqc_reference/reference_markers_gtdb.fasta -out GCF_007641235.1_ASM764123v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:39,230] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:39,234] [INFO] Selected 10 target genomes.
[2024-01-24 13:43:39,234] [INFO] Target genome list was writen to GCF_007641235.1_ASM764123v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:39,262] [INFO] Task started: fastANI
[2024-01-24 13:43:39,263] [INFO] Running command: fastANI --query /var/lib/cwl/stg0ccb726c-5bbf-4ca7-b6ec-3f15a5e93943/GCF_007641235.1_ASM764123v1_genomic.fna.gz --refList GCF_007641235.1_ASM764123v1_genomic.fna/target_genomes_gtdb.txt --output GCF_007641235.1_ASM764123v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:43:44,759] [INFO] Task succeeded: fastANI
[2024-01-24 13:43:44,772] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:43:44,773] [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_007641235.1	s__Corynebacterium sanguinis	100.0	785	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.90	0.92	0.90	7	conclusive
GCF_000159635.1	s__Corynebacterium lipophiloflavum	92.407	665	787	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	83.9171	586	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_011038645.2	s__Corynebacterium qintianiae	83.5241	550	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.90	98.90	0.92	0.92	2	-
GCF_003070865.1	s__Corynebacterium liangguodongii	82.1295	502	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.99	99.99	1.00	1.00	2	-
GCF_900411315.1	s__Corynebacterium senegalense	81.8426	526	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013978595.1	s__Corynebacterium haemomassiliense	80.7271	427	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002339505.1	s__Corynebacterium sp002339505	80.598	456	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015351335.1	s__Corynebacterium lipophilum	80.3596	388	787	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	80.2147	396	787	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.27	97.60	0.93	0.89	5	-
--------------------------------------------------------------------------------
[2024-01-24 13:43:44,774] [INFO] GTDB search result was written to GCF_007641235.1_ASM764123v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:43:44,774] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:43:44,777] [INFO] DFAST_QC result json was written to GCF_007641235.1_ASM764123v1_genomic.fna/dqc_result.json
[2024-01-24 13:43:44,778] [INFO] DFAST_QC completed!
[2024-01-24 13:43:44,778] [INFO] Total running time: 0h0m48s