[2024-01-25 19:50:20,623] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:50:20,629] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:50:20,629] [INFO] DQC Reference Directory: /var/lib/cwl/stgaa60459d-c7b2-4c57-86f8-096e98afabe4/dqc_reference
[2024-01-25 19:50:21,734] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:50:21,734] [INFO] Task started: Prodigal
[2024-01-25 19:50:21,735] [INFO] Running command: gunzip -c /var/lib/cwl/stg8ca15080-b764-4fc1-bd39-bfd2e515bd13/GCF_025821305.1_ASM2582130v1_genomic.fna.gz | prodigal -d GCF_025821305.1_ASM2582130v1_genomic.fna/cds.fna -a GCF_025821305.1_ASM2582130v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:50:36,005] [INFO] Task succeeded: Prodigal
[2024-01-25 19:50:36,005] [INFO] Task started: HMMsearch
[2024-01-25 19:50:36,005] [INFO] Running command: hmmsearch --tblout GCF_025821305.1_ASM2582130v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaa60459d-c7b2-4c57-86f8-096e98afabe4/dqc_reference/reference_markers.hmm GCF_025821305.1_ASM2582130v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:50:36,282] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:50:36,283] [INFO] Found 6/6 markers.
[2024-01-25 19:50:36,325] [INFO] Query marker FASTA was written to GCF_025821305.1_ASM2582130v1_genomic.fna/markers.fasta
[2024-01-25 19:50:36,325] [INFO] Task started: Blastn
[2024-01-25 19:50:36,325] [INFO] Running command: blastn -query GCF_025821305.1_ASM2582130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa60459d-c7b2-4c57-86f8-096e98afabe4/dqc_reference/reference_markers.fasta -out GCF_025821305.1_ASM2582130v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:50:37,373] [INFO] Task succeeded: Blastn
[2024-01-25 19:50:37,376] [INFO] Selected 13 target genomes.
[2024-01-25 19:50:37,376] [INFO] Target genome list was writen to GCF_025821305.1_ASM2582130v1_genomic.fna/target_genomes.txt
[2024-01-25 19:50:37,390] [INFO] Task started: fastANI
[2024-01-25 19:50:37,390] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ca15080-b764-4fc1-bd39-bfd2e515bd13/GCF_025821305.1_ASM2582130v1_genomic.fna.gz --refList GCF_025821305.1_ASM2582130v1_genomic.fna/target_genomes.txt --output GCF_025821305.1_ASM2582130v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:50:52,753] [INFO] Task succeeded: fastANI
[2024-01-25 19:50:52,754] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaa60459d-c7b2-4c57-86f8-096e98afabe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:50:52,754] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaa60459d-c7b2-4c57-86f8-096e98afabe4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:50:52,763] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:50:52,763] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:50:52,763] [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 noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	99.9935	1553	1558	95	conclusive
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	99.956	1491	1558	95	conclusive
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	84.2157	1151	1558	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	84.1875	1144	1558	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	84.1718	1127	1558	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	83.7788	1156	1558	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	81.795	796	1558	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	81.7916	1031	1558	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	81.0212	1020	1558	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	80.6233	899	1558	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.6043	939	1558	95	below_threshold
Mycobacterium sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	79.4486	779	1558	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	79.3718	760	1558	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:50:52,764] [INFO] DFAST Taxonomy check result was written to GCF_025821305.1_ASM2582130v1_genomic.fna/tc_result.tsv
[2024-01-25 19:50:52,765] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:50:52,765] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:50:52,765] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaa60459d-c7b2-4c57-86f8-096e98afabe4/dqc_reference/checkm_data
[2024-01-25 19:50:52,766] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:50:52,811] [INFO] Task started: CheckM
[2024-01-25 19:50:52,811] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025821305.1_ASM2582130v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025821305.1_ASM2582130v1_genomic.fna/checkm_input GCF_025821305.1_ASM2582130v1_genomic.fna/checkm_result
[2024-01-25 19:51:33,079] [INFO] Task succeeded: CheckM
[2024-01-25 19:51:33,080] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:51:33,099] [INFO] ===== Completeness check finished =====
[2024-01-25 19:51:33,099] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:51:33,100] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025821305.1_ASM2582130v1_genomic.fna/markers.fasta)
[2024-01-25 19:51:33,100] [INFO] Task started: Blastn
[2024-01-25 19:51:33,100] [INFO] Running command: blastn -query GCF_025821305.1_ASM2582130v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaa60459d-c7b2-4c57-86f8-096e98afabe4/dqc_reference/reference_markers_gtdb.fasta -out GCF_025821305.1_ASM2582130v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:51:34,587] [INFO] Task succeeded: Blastn
[2024-01-25 19:51:34,589] [INFO] Selected 19 target genomes.
[2024-01-25 19:51:34,589] [INFO] Target genome list was writen to GCF_025821305.1_ASM2582130v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:51:34,610] [INFO] Task started: fastANI
[2024-01-25 19:51:34,610] [INFO] Running command: fastANI --query /var/lib/cwl/stg8ca15080-b764-4fc1-bd39-bfd2e515bd13/GCF_025821305.1_ASM2582130v1_genomic.fna.gz --refList GCF_025821305.1_ASM2582130v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025821305.1_ASM2582130v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:51:55,976] [INFO] Task succeeded: fastANI
[2024-01-25 19:51:55,987] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:51:55,988] [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_010731635.1	s__Mycobacterium noviomagense	99.9935	1553	1558	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_009936235.1	s__Mycobacterium xenopi	84.2116	1152	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.67	99.09	0.97	0.94	5	-
GCF_016592155.1	s__Mycobacterium heckeshornense	83.7837	1156	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.54	99.17	0.94	0.93	4	-
GCF_002101735.1	s__Mycobacterium kyorinense	81.8112	1031	1558	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	81.7999	1034	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101595.1	s__Mycobacterium celatum	81.7591	1038	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_002102185.1	s__Mycobacterium fragae	81.029	1018	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086305.1	s__Mycobacterium malmoense_B	80.7529	877	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001672775.1	s__Mycobacterium kyorinense_A	80.6891	901	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002101815.1	s__Mycobacterium paraense	80.6511	931	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_003284935.1	s__Mycobacterium arosiense_A	80.3173	817	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001667035.1	s__Mycobacterium sp001667035	80.2905	900	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001954275.1	s__Mycobacterium sp001954275	80.2496	889	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	80.134	828	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_010730055.1	s__Mycobacterium shinjukuense	80.0605	730	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001665875.1	s__Mycobacterium sp001665875	79.6705	838	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001668625.1	s__Mycobacterium sp001668625	79.6507	642	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102355.1	s__Mycobacterium sherrisii	79.4495	777	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.78	99.78	0.96	0.96	2	-
GCF_010727605.1	s__Mycobacterium simiae	79.3664	763	1558	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:51:55,989] [INFO] GTDB search result was written to GCF_025821305.1_ASM2582130v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:51:55,990] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:51:55,993] [INFO] DFAST_QC result json was written to GCF_025821305.1_ASM2582130v1_genomic.fna/dqc_result.json
[2024-01-25 19:51:55,993] [INFO] DFAST_QC completed!
[2024-01-25 19:51:55,993] [INFO] Total running time: 0h1m35s