[2024-01-24 12:15:20,563] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:15:20,565] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:15:20,565] [INFO] DQC Reference Directory: /var/lib/cwl/stg9a79ec8f-85c6-4df2-815d-c37adf904983/dqc_reference
[2024-01-24 12:15:21,845] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:15:21,846] [INFO] Task started: Prodigal
[2024-01-24 12:15:21,846] [INFO] Running command: gunzip -c /var/lib/cwl/stgabf77aa3-d2ef-49a8-b912-54eac1372a27/GCF_030408735.1_ASM3040873v1_genomic.fna.gz | prodigal -d GCF_030408735.1_ASM3040873v1_genomic.fna/cds.fna -a GCF_030408735.1_ASM3040873v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:15:33,220] [INFO] Task succeeded: Prodigal
[2024-01-24 12:15:33,220] [INFO] Task started: HMMsearch
[2024-01-24 12:15:33,220] [INFO] Running command: hmmsearch --tblout GCF_030408735.1_ASM3040873v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9a79ec8f-85c6-4df2-815d-c37adf904983/dqc_reference/reference_markers.hmm GCF_030408735.1_ASM3040873v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:15:33,469] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:15:33,471] [INFO] Found 6/6 markers.
[2024-01-24 12:15:33,503] [INFO] Query marker FASTA was written to GCF_030408735.1_ASM3040873v1_genomic.fna/markers.fasta
[2024-01-24 12:15:33,504] [INFO] Task started: Blastn
[2024-01-24 12:15:33,504] [INFO] Running command: blastn -query GCF_030408735.1_ASM3040873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a79ec8f-85c6-4df2-815d-c37adf904983/dqc_reference/reference_markers.fasta -out GCF_030408735.1_ASM3040873v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:15:34,354] [INFO] Task succeeded: Blastn
[2024-01-24 12:15:34,357] [INFO] Selected 12 target genomes.
[2024-01-24 12:15:34,358] [INFO] Target genome list was writen to GCF_030408735.1_ASM3040873v1_genomic.fna/target_genomes.txt
[2024-01-24 12:15:34,363] [INFO] Task started: fastANI
[2024-01-24 12:15:34,363] [INFO] Running command: fastANI --query /var/lib/cwl/stgabf77aa3-d2ef-49a8-b912-54eac1372a27/GCF_030408735.1_ASM3040873v1_genomic.fna.gz --refList GCF_030408735.1_ASM3040873v1_genomic.fna/target_genomes.txt --output GCF_030408735.1_ASM3040873v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:15:41,271] [INFO] Task succeeded: fastANI
[2024-01-24 12:15:41,272] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9a79ec8f-85c6-4df2-815d-c37adf904983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:15:41,273] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9a79ec8f-85c6-4df2-815d-c37adf904983/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:15:41,284] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 12:15:41,284] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 12:15:41,285] [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 gallinarum	strain=Sa1YVA5	GCA_014837045.1	2762214	2762214	type	True	83.5778	748	1046	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000011305.1	152794	152794	type	True	83.1847	755	1046	95	below_threshold
Corynebacterium efficiens	strain=YS-314	GCA_000160795.1	152794	152794	type	True	83.0498	743	1046	95	below_threshold
Corynebacterium crudilactis	strain=JZ16	GCA_001643015.1	1652495	1652495	type	True	79.6409	306	1046	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_002847405.1	1718	1718	type	True	79.5864	352	1046	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_000011325.1	1718	1718	type	True	79.5193	364	1046	95	below_threshold
Corynebacterium occultum	strain=2039	GCA_009734425.1	2675219	2675219	type	True	79.3749	354	1046	95	below_threshold
Corynebacterium suranareeae	strain=N24	GCA_002355155.1	2506452	2506452	type	True	79.3584	294	1046	95	below_threshold
Corynebacterium glutamicum	strain=ATCC 13032	GCA_011761195.1	1718	1718	type	True	79.3428	369	1046	95	below_threshold
Corynebacterium marinum	strain=CGMCC 1.6998	GCA_014645275.1	349751	349751	type	True	79.1013	306	1046	95	below_threshold
Corynebacterium pollutisoli	strain=VDS11	GCA_900177745.1	1610489	1610489	type	True	78.6586	301	1046	95	below_threshold
Corynebacterium fournieri	strain=Marseille-P2948	GCA_900176865.1	1852390	1852390	type	True	77.5594	160	1046	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:15:41,286] [INFO] DFAST Taxonomy check result was written to GCF_030408735.1_ASM3040873v1_genomic.fna/tc_result.tsv
[2024-01-24 12:15:41,287] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:15:41,287] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:15:41,287] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9a79ec8f-85c6-4df2-815d-c37adf904983/dqc_reference/checkm_data
[2024-01-24 12:15:41,288] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:15:41,324] [INFO] Task started: CheckM
[2024-01-24 12:15:41,325] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_030408735.1_ASM3040873v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_030408735.1_ASM3040873v1_genomic.fna/checkm_input GCF_030408735.1_ASM3040873v1_genomic.fna/checkm_result
[2024-01-24 12:16:18,391] [INFO] Task succeeded: CheckM
[2024-01-24 12:16:18,392] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.54%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:16:18,413] [INFO] ===== Completeness check finished =====
[2024-01-24 12:16:18,414] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:16:18,414] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_030408735.1_ASM3040873v1_genomic.fna/markers.fasta)
[2024-01-24 12:16:18,415] [INFO] Task started: Blastn
[2024-01-24 12:16:18,415] [INFO] Running command: blastn -query GCF_030408735.1_ASM3040873v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9a79ec8f-85c6-4df2-815d-c37adf904983/dqc_reference/reference_markers_gtdb.fasta -out GCF_030408735.1_ASM3040873v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:16:19,650] [INFO] Task succeeded: Blastn
[2024-01-24 12:16:19,654] [INFO] Selected 14 target genomes.
[2024-01-24 12:16:19,655] [INFO] Target genome list was writen to GCF_030408735.1_ASM3040873v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:16:19,665] [INFO] Task started: fastANI
[2024-01-24 12:16:19,665] [INFO] Running command: fastANI --query /var/lib/cwl/stgabf77aa3-d2ef-49a8-b912-54eac1372a27/GCF_030408735.1_ASM3040873v1_genomic.fna.gz --refList GCF_030408735.1_ASM3040873v1_genomic.fna/target_genomes_gtdb.txt --output GCF_030408735.1_ASM3040873v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:16:27,352] [INFO] Task succeeded: fastANI
[2024-01-24 12:16:27,377] [INFO] Found 14 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 12:16:27,377] [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_014837045.1	s__Corynebacterium sp014837045	83.572	747	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011305.1	s__Corynebacterium efficiens	83.1657	754	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.90	99.90	0.99	0.99	2	-
GCF_000344785.1	s__Corynebacterium callunae	79.8798	296	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001277995.1	s__Corynebacterium deserti	79.7435	331	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001643015.1	s__Corynebacterium crudilactis	79.5957	305	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000011325.1	s__Corynebacterium glutamicum	79.5101	363	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.67	97.34	0.92	0.85	76	-
GCF_002355155.1	s__Corynebacterium suranareeae	79.3584	294	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000835165.1	s__Corynebacterium marinum	79.1514	316	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	99.21	98.42	0.97	0.94	3	-
GCF_900169525.1	s__Corynebacterium pacaense	79.0572	388	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_003955685.1	s__Corynebacterium sp003955685	78.8154	347	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900177745.1	s__Corynebacterium pollutisoli	78.6446	302	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	98.83	98.83	0.98	0.98	2	-
GCA_012838985.1	s__Corynebacterium sp012838985	78.1004	238	1046	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	77.5622	160	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003693265.1	s__Corynebacterium gottingense	77.5392	143	1046	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Corynebacterium	95.0	97.52	97.05	0.92	0.90	11	-
--------------------------------------------------------------------------------
[2024-01-24 12:16:27,378] [INFO] GTDB search result was written to GCF_030408735.1_ASM3040873v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:16:27,379] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:16:27,382] [INFO] DFAST_QC result json was written to GCF_030408735.1_ASM3040873v1_genomic.fna/dqc_result.json
[2024-01-24 12:16:27,383] [INFO] DFAST_QC completed!
[2024-01-24 12:16:27,383] [INFO] Total running time: 0h1m7s