[2024-01-25 20:05:20,573] [INFO] DFAST_QC pipeline started.
[2024-01-25 20:05:20,575] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 20:05:20,575] [INFO] DQC Reference Directory: /var/lib/cwl/stg110d0805-a086-4dc0-bb7b-ada3cea149ff/dqc_reference
[2024-01-25 20:05:21,795] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 20:05:21,796] [INFO] Task started: Prodigal
[2024-01-25 20:05:21,796] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcc2ccc4-08aa-4ecf-8371-d8c61dee4459/GCF_030408615.1_ASM3040861v1_genomic.fna.gz | prodigal -d GCF_030408615.1_ASM3040861v1_genomic.fna/cds.fna -a GCF_030408615.1_ASM3040861v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 20:05:28,710] [INFO] Task succeeded: Prodigal
[2024-01-25 20:05:28,710] [INFO] Task started: HMMsearch
[2024-01-25 20:05:28,710] [INFO] Running command: hmmsearch --tblout GCF_030408615.1_ASM3040861v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg110d0805-a086-4dc0-bb7b-ada3cea149ff/dqc_reference/reference_markers.hmm GCF_030408615.1_ASM3040861v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 20:05:28,931] [INFO] Task succeeded: HMMsearch
[2024-01-25 20:05:28,932] [INFO] Found 6/6 markers.
[2024-01-25 20:05:28,955] [INFO] Query marker FASTA was written to GCF_030408615.1_ASM3040861v1_genomic.fna/markers.fasta
[2024-01-25 20:05:28,955] [INFO] Task started: Blastn
[2024-01-25 20:05:28,955] [INFO] Running command: blastn -query GCF_030408615.1_ASM3040861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg110d0805-a086-4dc0-bb7b-ada3cea149ff/dqc_reference/reference_markers.fasta -out GCF_030408615.1_ASM3040861v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:05:30,024] [INFO] Task succeeded: Blastn
[2024-01-25 20:05:30,027] [INFO] Selected 8 target genomes.
[2024-01-25 20:05:30,027] [INFO] Target genome list was writen to GCF_030408615.1_ASM3040861v1_genomic.fna/target_genomes.txt
[2024-01-25 20:05:30,035] [INFO] Task started: fastANI
[2024-01-25 20:05:30,035] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc2ccc4-08aa-4ecf-8371-d8c61dee4459/GCF_030408615.1_ASM3040861v1_genomic.fna.gz --refList GCF_030408615.1_ASM3040861v1_genomic.fna/target_genomes.txt --output GCF_030408615.1_ASM3040861v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 20:05:34,774] [INFO] Task succeeded: fastANI
[2024-01-25 20:05:34,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg110d0805-a086-4dc0-bb7b-ada3cea149ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 20:05:34,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg110d0805-a086-4dc0-bb7b-ada3cea149ff/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 20:05:34,781] [INFO] Found 8 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 20:05:34,781] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 20:05:34,781] [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 bovis	strain=DSM 20582	GCA_014191555.1	36808	36808	type	True	99.9932	875	883	95	conclusive
Corynebacterium bovis	strain=FDAARGOS_1052	GCA_016128075.1	36808	36808	type	True	99.983	881	883	95	conclusive
Corynebacterium bovis	strain=DSM 20582	GCA_000183325.2	36808	36808	type	True	99.5872	592	883	95	conclusive
Corynebacterium nuruki	strain=S6-4	GCA_007970465.1	1032851	1032851	type	True	79.8997	417	883	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_000213935.2	1032851	1032851	type	True	79.7371	417	883	95	below_threshold
Corynebacterium variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	79.1253	379	883	95	below_threshold
Corynebacterium frankenforstense	strain=ST18	GCA_001941485.1	1230998	1230998	type	True	78.5078	341	883	95	below_threshold
Corynebacterium phoceense	strain=MC1	GCA_900092335.1	1686286	1686286	type	True	77.2103	181	883	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 20:05:34,783] [INFO] DFAST Taxonomy check result was written to GCF_030408615.1_ASM3040861v1_genomic.fna/tc_result.tsv
[2024-01-25 20:05:34,784] [INFO] ===== Taxonomy check completed =====
[2024-01-25 20:05:34,784] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 20:05:34,784] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg110d0805-a086-4dc0-bb7b-ada3cea149ff/dqc_reference/checkm_data
[2024-01-25 20:05:34,785] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 20:05:34,814] [INFO] Task started: CheckM
[2024-01-25 20:05:34,814] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408615.1_ASM3040861v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408615.1_ASM3040861v1_genomic.fna/checkm_input GCF_030408615.1_ASM3040861v1_genomic.fna/checkm_result
[2024-01-25 20:06:18,048] [INFO] Task succeeded: CheckM
[2024-01-25 20:06:18,050] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 20:06:18,065] [INFO] ===== Completeness check finished =====
[2024-01-25 20:06:18,066] [INFO] ===== Start GTDB Search =====
[2024-01-25 20:06:18,067] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408615.1_ASM3040861v1_genomic.fna/markers.fasta)
[2024-01-25 20:06:18,067] [INFO] Task started: Blastn
[2024-01-25 20:06:18,067] [INFO] Running command: blastn -query GCF_030408615.1_ASM3040861v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg110d0805-a086-4dc0-bb7b-ada3cea149ff/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408615.1_ASM3040861v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 20:06:19,724] [INFO] Task succeeded: Blastn
[2024-01-25 20:06:19,729] [INFO] Selected 13 target genomes.
[2024-01-25 20:06:19,729] [INFO] Target genome list was writen to GCF_030408615.1_ASM3040861v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 20:06:19,739] [INFO] Task started: fastANI
[2024-01-25 20:06:19,739] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcc2ccc4-08aa-4ecf-8371-d8c61dee4459/GCF_030408615.1_ASM3040861v1_genomic.fna.gz --refList GCF_030408615.1_ASM3040861v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408615.1_ASM3040861v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 20:06:28,063] [INFO] Task succeeded: fastANI
[2024-01-25 20:06:28,072] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 20:06:28,073] [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_000183325.1	s__Corynebacterium bovis	99.5872	592	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.01	98.42	0.92	0.83	23	conclusive
GCF_007970465.1	s__Corynebacterium nuruki	79.9359	418	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.35	98.70	0.99	0.98	3	-
GCA_019120175.1	s__Corynebacterium faecigallinarum	79.1532	344	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006539825.1	s__Corynebacterium variabile	79.1366	378	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.53	98.15	0.92	0.86	8	-
GCF_000418365.1	s__Corynebacterium terpenotabidum	79.1182	334	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_902782855.1	s__Corynebacterium sp902782855	78.7743	317	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_019114135.1	s__Corynebacterium avicola	78.6985	355	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001942345.1	s__Corynebacterium sp001942345	78.4786	324	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001941485.1	s__Corynebacterium frankenforstense	78.456	341	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007673095.1	s__Corynebacterium sp002363255	78.3395	334	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.44	97.44	0.87	0.87	2	-
GCF_900092335.1	s__Corynebacterium phoceense	77.2392	179	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.96	96.08	0.95	0.92	11	-
GCF_009858245.1	s__Ornithinibacter aureus	76.57	157	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Dermatophilaceae;g__Ornithinibacter	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013778455.1	s__Streptomyces himalayensis	75.853	217	883	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	97.53	97.53	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-25 20:06:28,074] [INFO] GTDB search result was written to GCF_030408615.1_ASM3040861v1_genomic.fna/result_gtdb.tsv
[2024-01-25 20:06:28,074] [INFO] ===== GTDB Search completed =====
[2024-01-25 20:06:28,077] [INFO] DFAST_QC result json was written to GCF_030408615.1_ASM3040861v1_genomic.fna/dqc_result.json
[2024-01-25 20:06:28,077] [INFO] DFAST_QC completed!
[2024-01-25 20:06:28,077] [INFO] Total running time: 0h1m8s