[2024-01-24 14:22:44,577] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:22:44,578] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:22:44,579] [INFO] DQC Reference Directory: /var/lib/cwl/stgd3b49f12-6323-4327-95a3-638b1764e619/dqc_reference
[2024-01-24 14:22:45,774] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:22:45,775] [INFO] Task started: Prodigal
[2024-01-24 14:22:45,775] [INFO] Running command: gunzip -c /var/lib/cwl/stg2d27ff50-a1ab-4975-a7c2-cd3f8ff2ef5e/GCF_025822465.1_ASM2582246v1_genomic.fna.gz | prodigal -d GCF_025822465.1_ASM2582246v1_genomic.fna/cds.fna -a GCF_025822465.1_ASM2582246v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:23:06,832] [INFO] Task succeeded: Prodigal
[2024-01-24 14:23:06,833] [INFO] Task started: HMMsearch
[2024-01-24 14:23:06,833] [INFO] Running command: hmmsearch --tblout GCF_025822465.1_ASM2582246v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgd3b49f12-6323-4327-95a3-638b1764e619/dqc_reference/reference_markers.hmm GCF_025822465.1_ASM2582246v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:23:07,210] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:23:07,211] [INFO] Found 6/6 markers.
[2024-01-24 14:23:07,263] [INFO] Query marker FASTA was written to GCF_025822465.1_ASM2582246v1_genomic.fna/markers.fasta
[2024-01-24 14:23:07,263] [INFO] Task started: Blastn
[2024-01-24 14:23:07,263] [INFO] Running command: blastn -query GCF_025822465.1_ASM2582246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b49f12-6323-4327-95a3-638b1764e619/dqc_reference/reference_markers.fasta -out GCF_025822465.1_ASM2582246v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:23:08,341] [INFO] Task succeeded: Blastn
[2024-01-24 14:23:08,346] [INFO] Selected 11 target genomes.
[2024-01-24 14:23:08,346] [INFO] Target genome list was writen to GCF_025822465.1_ASM2582246v1_genomic.fna/target_genomes.txt
[2024-01-24 14:23:08,375] [INFO] Task started: fastANI
[2024-01-24 14:23:08,375] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d27ff50-a1ab-4975-a7c2-cd3f8ff2ef5e/GCF_025822465.1_ASM2582246v1_genomic.fna.gz --refList GCF_025822465.1_ASM2582246v1_genomic.fna/target_genomes.txt --output GCF_025822465.1_ASM2582246v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:23:22,433] [INFO] Task succeeded: fastANI
[2024-01-24 14:23:22,433] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgd3b49f12-6323-4327-95a3-638b1764e619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:23:22,434] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgd3b49f12-6323-4327-95a3-638b1764e619/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:23:22,445] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 14:23:22,445] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:23:22,446] [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
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	99.9958	1948	1948	95	conclusive
Mycobacterium branderi	strain=DSM 44624	GCA_002086575.1	43348	43348	type	True	99.9835	1923	1948	95	conclusive
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	90.8923	1338	1948	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	90.891	1372	1948	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	90.8336	1350	1948	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	90.543	1018	1948	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	82.6427	1130	1948	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	81.68	1045	1948	95	below_threshold
Mycolicibacter kumamotonensis	strain=DSM 45093	GCA_002086285.1	354243	354243	type	True	80.3145	794	1948	95	below_threshold
Mycolicibacter senuensis	strain=DSM 44999	GCA_002101885.1	386913	386913	type	True	80.2909	789	1948	95	below_threshold
Mycolicibacter senuensis	strain=JCM 16017	GCA_010723225.1	386913	386913	type	True	80.2834	814	1948	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:23:22,447] [INFO] DFAST Taxonomy check result was written to GCF_025822465.1_ASM2582246v1_genomic.fna/tc_result.tsv
[2024-01-24 14:23:22,448] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:23:22,449] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:23:22,449] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgd3b49f12-6323-4327-95a3-638b1764e619/dqc_reference/checkm_data
[2024-01-24 14:23:22,450] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:23:22,527] [INFO] Task started: CheckM
[2024-01-24 14:23:22,527] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822465.1_ASM2582246v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822465.1_ASM2582246v1_genomic.fna/checkm_input GCF_025822465.1_ASM2582246v1_genomic.fna/checkm_result
[2024-01-24 14:24:25,806] [INFO] Task succeeded: CheckM
[2024-01-24 14:24:25,808] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:24:25,831] [INFO] ===== Completeness check finished =====
[2024-01-24 14:24:25,832] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:24:25,832] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822465.1_ASM2582246v1_genomic.fna/markers.fasta)
[2024-01-24 14:24:25,833] [INFO] Task started: Blastn
[2024-01-24 14:24:25,833] [INFO] Running command: blastn -query GCF_025822465.1_ASM2582246v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgd3b49f12-6323-4327-95a3-638b1764e619/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822465.1_ASM2582246v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:24:27,447] [INFO] Task succeeded: Blastn
[2024-01-24 14:24:27,450] [INFO] Selected 11 target genomes.
[2024-01-24 14:24:27,450] [INFO] Target genome list was writen to GCF_025822465.1_ASM2582246v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:24:27,459] [INFO] Task started: fastANI
[2024-01-24 14:24:27,459] [INFO] Running command: fastANI --query /var/lib/cwl/stg2d27ff50-a1ab-4975-a7c2-cd3f8ff2ef5e/GCF_025822465.1_ASM2582246v1_genomic.fna.gz --refList GCF_025822465.1_ASM2582246v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822465.1_ASM2582246v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:24:41,556] [INFO] Task succeeded: fastANI
[2024-01-24 14:24:41,576] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:24:41,577] [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_010728725.1	s__Mycobacterium branderi	99.9958	1948	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_002101595.1	s__Mycobacterium celatum	90.8963	1337	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002101735.1	s__Mycobacterium kyorinense	90.8794	1373	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_003402475.1	s__Mycobacterium sp003402475	90.0666	1390	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672775.1	s__Mycobacterium kyorinense_A	83.0098	1132	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002101905.1	s__Mycobacterium shimoidei	82.7244	1050	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.72	99.46	0.97	0.95	3	-
GCF_002102185.1	s__Mycobacterium fragae	82.6538	1128	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000277125.1	s__Mycobacterium intracellulare	81.0725	981	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCF_001667945.1	s__Mycobacterium sinense_B	80.3426	778	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.61	99.42	0.94	0.94	3	-
GCF_002101885.1	s__Mycobacterium senuense	80.2852	791	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_001667375.1	s__Mycobacterium sinense_A	80.1731	824	1948	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.51	95.04	0.94	0.89	3	-
--------------------------------------------------------------------------------
[2024-01-24 14:24:41,579] [INFO] GTDB search result was written to GCF_025822465.1_ASM2582246v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:24:41,580] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:24:41,584] [INFO] DFAST_QC result json was written to GCF_025822465.1_ASM2582246v1_genomic.fna/dqc_result.json
[2024-01-24 14:24:41,584] [INFO] DFAST_QC completed!
[2024-01-24 14:24:41,584] [INFO] Total running time: 0h1m57s