[2024-01-24 12:06:14,098] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:14,100] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:14,100] [INFO] DQC Reference Directory: /var/lib/cwl/stg67c777aa-de5f-4aba-aef1-82f7a92d837a/dqc_reference
[2024-01-24 12:06:15,424] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:15,425] [INFO] Task started: Prodigal
[2024-01-24 12:06:15,425] [INFO] Running command: gunzip -c /var/lib/cwl/stg5498da94-e1d7-47eb-be87-ed19557ff4c1/GCF_006539825.1_ASM653982v1_genomic.fna.gz | prodigal -d GCF_006539825.1_ASM653982v1_genomic.fna/cds.fna -a GCF_006539825.1_ASM653982v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:25,177] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:25,177] [INFO] Task started: HMMsearch
[2024-01-24 12:06:25,177] [INFO] Running command: hmmsearch --tblout GCF_006539825.1_ASM653982v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg67c777aa-de5f-4aba-aef1-82f7a92d837a/dqc_reference/reference_markers.hmm GCF_006539825.1_ASM653982v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:25,441] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:25,443] [INFO] Found 6/6 markers.
[2024-01-24 12:06:25,489] [INFO] Query marker FASTA was written to GCF_006539825.1_ASM653982v1_genomic.fna/markers.fasta
[2024-01-24 12:06:25,489] [INFO] Task started: Blastn
[2024-01-24 12:06:25,489] [INFO] Running command: blastn -query GCF_006539825.1_ASM653982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c777aa-de5f-4aba-aef1-82f7a92d837a/dqc_reference/reference_markers.fasta -out GCF_006539825.1_ASM653982v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:26,540] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:26,547] [INFO] Selected 9 target genomes.
[2024-01-24 12:06:26,547] [INFO] Target genome list was writen to GCF_006539825.1_ASM653982v1_genomic.fna/target_genomes.txt
[2024-01-24 12:06:26,551] [INFO] Task started: fastANI
[2024-01-24 12:06:26,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg5498da94-e1d7-47eb-be87-ed19557ff4c1/GCF_006539825.1_ASM653982v1_genomic.fna.gz --refList GCF_006539825.1_ASM653982v1_genomic.fna/target_genomes.txt --output GCF_006539825.1_ASM653982v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:06:31,957] [INFO] Task succeeded: fastANI
[2024-01-24 12:06:31,958] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg67c777aa-de5f-4aba-aef1-82f7a92d837a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:06:31,958] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg67c777aa-de5f-4aba-aef1-82f7a92d837a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:06:31,967] [INFO] Found 9 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:06:31,967] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:06:31,967] [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 variabile	strain=NBRC 15286	GCA_006539825.1	1727	1727	type	True	100.0	1026	1029	95	conclusive
Corynebacterium terpenotabidum	strain=Y-11	GCA_000418365.1	89154	89154	type	True	83.6693	710	1029	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_000213935.2	1032851	1032851	type	True	82.9112	664	1029	95	below_threshold
Corynebacterium nuruki	strain=S6-4	GCA_007970465.1	1032851	1032851	type	True	82.7979	698	1029	95	below_threshold
Corynebacterium neomassiliense	strain=Marseille-P3888	GCA_900626215.1	2079482	2079482	type	True	81.2099	655	1029	95	below_threshold
Corynebacterium humireducens	strain=NBRC 106098	GCA_001571025.1	1223514	1223514	type	True	79.1465	298	1029	95	below_threshold
Corynebacterium humireducens	strain=DSM 45392	GCA_000819445.1	1223514	1223514	type	True	79.0904	306	1029	95	below_threshold
Corynebacterium urealyticum	strain=FDAARGOS_994	GCA_016127975.1	43771	43771	type	True	78.8566	253	1029	95	below_threshold
Corynebacterium gallinarum	strain=Sa1YVA5	GCA_014837045.1	2762214	2762214	type	True	78.2248	238	1029	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:06:31,968] [INFO] DFAST Taxonomy check result was written to GCF_006539825.1_ASM653982v1_genomic.fna/tc_result.tsv
[2024-01-24 12:06:31,969] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:06:31,969] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:06:31,969] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg67c777aa-de5f-4aba-aef1-82f7a92d837a/dqc_reference/checkm_data
[2024-01-24 12:06:31,970] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:06:32,003] [INFO] Task started: CheckM
[2024-01-24 12:06:32,003] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006539825.1_ASM653982v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006539825.1_ASM653982v1_genomic.fna/checkm_input GCF_006539825.1_ASM653982v1_genomic.fna/checkm_result
[2024-01-24 12:07:04,725] [INFO] Task succeeded: CheckM
[2024-01-24 12:07:04,726] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:07:04,748] [INFO] ===== Completeness check finished =====
[2024-01-24 12:07:04,748] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:07:04,749] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006539825.1_ASM653982v1_genomic.fna/markers.fasta)
[2024-01-24 12:07:04,749] [INFO] Task started: Blastn
[2024-01-24 12:07:04,749] [INFO] Running command: blastn -query GCF_006539825.1_ASM653982v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg67c777aa-de5f-4aba-aef1-82f7a92d837a/dqc_reference/reference_markers_gtdb.fasta -out GCF_006539825.1_ASM653982v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:07:06,364] [INFO] Task succeeded: Blastn
[2024-01-24 12:07:06,368] [INFO] Selected 7 target genomes.
[2024-01-24 12:07:06,369] [INFO] Target genome list was writen to GCF_006539825.1_ASM653982v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:07:06,924] [INFO] Task started: fastANI
[2024-01-24 12:07:06,925] [INFO] Running command: fastANI --query /var/lib/cwl/stg5498da94-e1d7-47eb-be87-ed19557ff4c1/GCF_006539825.1_ASM653982v1_genomic.fna.gz --refList GCF_006539825.1_ASM653982v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006539825.1_ASM653982v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:07:11,959] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:11,975] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:07:11,976] [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_006539825.1	s__Corynebacterium variabile	100.0	1026	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.53	98.15	0.92	0.86	8	conclusive
GCA_902782855.1	s__Corynebacterium sp902782855	86.5121	657	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000418365.1	s__Corynebacterium terpenotabidum	83.6727	709	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007970465.1	s__Corynebacterium nuruki	82.7772	699	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.35	98.70	0.99	0.98	3	-
GCA_019114135.1	s__Corynebacterium avicola	81.4356	599	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900049755.1	s__Corynebacterium provencense	81.33	637	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.28	98.82	0.94	0.91	4	-
GCF_000819445.1	s__Corynebacterium humireducens	79.0904	306	1029	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.80	97.60	0.97	0.93	3	-
--------------------------------------------------------------------------------
[2024-01-24 12:07:11,978] [INFO] GTDB search result was written to GCF_006539825.1_ASM653982v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:07:11,979] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:07:11,984] [INFO] DFAST_QC result json was written to GCF_006539825.1_ASM653982v1_genomic.fna/dqc_result.json
[2024-01-24 12:07:11,984] [INFO] DFAST_QC completed!
[2024-01-24 12:07:11,985] [INFO] Total running time: 0h0m58s