[2024-01-24 11:05:27,799] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:27,804] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:27,805] [INFO] DQC Reference Directory: /var/lib/cwl/stg7bda85d6-9de9-405d-9941-3e3267e65cf7/dqc_reference
[2024-01-24 11:05:29,233] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:29,234] [INFO] Task started: Prodigal
[2024-01-24 11:05:29,234] [INFO] Running command: gunzip -c /var/lib/cwl/stgef529e31-6a5c-4607-a13a-98d0ad15b5c0/GCF_002086415.1_ASM208641v1_genomic.fna.gz | prodigal -d GCF_002086415.1_ASM208641v1_genomic.fna/cds.fna -a GCF_002086415.1_ASM208641v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:05:46,998] [INFO] Task succeeded: Prodigal
[2024-01-24 11:05:46,998] [INFO] Task started: HMMsearch
[2024-01-24 11:05:46,998] [INFO] Running command: hmmsearch --tblout GCF_002086415.1_ASM208641v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg7bda85d6-9de9-405d-9941-3e3267e65cf7/dqc_reference/reference_markers.hmm GCF_002086415.1_ASM208641v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:05:47,330] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:05:47,331] [INFO] Found 6/6 markers.
[2024-01-24 11:05:47,373] [INFO] Query marker FASTA was written to GCF_002086415.1_ASM208641v1_genomic.fna/markers.fasta
[2024-01-24 11:05:47,373] [INFO] Task started: Blastn
[2024-01-24 11:05:47,374] [INFO] Running command: blastn -query GCF_002086415.1_ASM208641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bda85d6-9de9-405d-9941-3e3267e65cf7/dqc_reference/reference_markers.fasta -out GCF_002086415.1_ASM208641v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:05:48,641] [INFO] Task succeeded: Blastn
[2024-01-24 11:05:48,645] [INFO] Selected 13 target genomes.
[2024-01-24 11:05:48,645] [INFO] Target genome list was writen to GCF_002086415.1_ASM208641v1_genomic.fna/target_genomes.txt
[2024-01-24 11:05:48,651] [INFO] Task started: fastANI
[2024-01-24 11:05:48,651] [INFO] Running command: fastANI --query /var/lib/cwl/stgef529e31-6a5c-4607-a13a-98d0ad15b5c0/GCF_002086415.1_ASM208641v1_genomic.fna.gz --refList GCF_002086415.1_ASM208641v1_genomic.fna/target_genomes.txt --output GCF_002086415.1_ASM208641v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:03,672] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:03,672] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg7bda85d6-9de9-405d-9941-3e3267e65cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:03,672] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg7bda85d6-9de9-405d-9941-3e3267e65cf7/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:03,685] [INFO] Found 13 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 11:06:03,685] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:03,686] [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=DSM 45145	GCA_002086415.1	459858	459858	type	True	100.0	1508	1511	95	conclusive
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	99.9956	1511	1511	95	conclusive
Mycobacterium xenopi	strain=JCM 15661T	GCA_009936235.1	1789	1789	type	True	84.2552	1116	1511	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	84.2489	1107	1511	95	below_threshold
Mycobacterium xenopi	strain=NCTC10042	GCA_900453395.1	1789	1789	type	True	84.2039	1134	1511	95	below_threshold
Mycobacterium heckeshornense	strain=JCM 15655	GCA_016592155.1	110505	110505	type	True	83.8208	1120	1511	95	below_threshold
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	81.7936	1016	1511	95	below_threshold
Mycobacterium celatum	strain=ATCC 51131	GCA_000974705.1	28045	28045	type	True	81.7405	773	1511	95	below_threshold
Mycobacterium fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	81.1266	969	1511	95	below_threshold
Mycobacterium paraense	strain=IEC26	GCA_002101815.1	767916	767916	type	True	80.6156	917	1511	95	below_threshold
Mycobacterium palustre	strain=DSM 44572	GCA_002101785.1	153971	153971	type	True	80.508	887	1511	95	below_threshold
Mycobacterium sherrisii	strain=ATCC BAA-832	GCA_002102355.1	243061	243061	type	True	79.4365	778	1511	95	below_threshold
Mycobacterium simiae	strain=JCM 12377	GCA_010727605.1	1784	1784	type	True	79.3205	748	1511	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:03,697] [INFO] DFAST Taxonomy check result was written to GCF_002086415.1_ASM208641v1_genomic.fna/tc_result.tsv
[2024-01-24 11:06:03,698] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:03,698] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:03,698] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg7bda85d6-9de9-405d-9941-3e3267e65cf7/dqc_reference/checkm_data
[2024-01-24 11:06:03,700] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:03,748] [INFO] Task started: CheckM
[2024-01-24 11:06:03,748] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002086415.1_ASM208641v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002086415.1_ASM208641v1_genomic.fna/checkm_input GCF_002086415.1_ASM208641v1_genomic.fna/checkm_result
[2024-01-24 11:06:53,635] [INFO] Task succeeded: CheckM
[2024-01-24 11:06:53,636] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:06:53,660] [INFO] ===== Completeness check finished =====
[2024-01-24 11:06:53,660] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:06:53,661] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002086415.1_ASM208641v1_genomic.fna/markers.fasta)
[2024-01-24 11:06:53,661] [INFO] Task started: Blastn
[2024-01-24 11:06:53,661] [INFO] Running command: blastn -query GCF_002086415.1_ASM208641v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg7bda85d6-9de9-405d-9941-3e3267e65cf7/dqc_reference/reference_markers_gtdb.fasta -out GCF_002086415.1_ASM208641v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:55,222] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:55,225] [INFO] Selected 19 target genomes.
[2024-01-24 11:06:55,225] [INFO] Target genome list was writen to GCF_002086415.1_ASM208641v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:06:55,240] [INFO] Task started: fastANI
[2024-01-24 11:06:55,240] [INFO] Running command: fastANI --query /var/lib/cwl/stgef529e31-6a5c-4607-a13a-98d0ad15b5c0/GCF_002086415.1_ASM208641v1_genomic.fna.gz --refList GCF_002086415.1_ASM208641v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002086415.1_ASM208641v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:07:17,302] [INFO] Task succeeded: fastANI
[2024-01-24 11:07:17,325] [INFO] Found 19 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:07:17,325] [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	99.9956	1511	1511	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	84.2518	1115	1511	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	83.8289	1119	1511	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	81.8166	1018	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_002101595.1	s__Mycobacterium celatum	81.7738	1020	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	0.99	0.99	2	-
GCF_003402475.1	s__Mycobacterium sp003402475	81.708	1029	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002102185.1	s__Mycobacterium fragae	81.1348	968	1511	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	80.7456	881	1511	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	80.6274	914	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.85	98.84	0.95	0.95	4	-
GCF_002086305.1	s__Mycobacterium malmoense_B	80.6131	877	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.01	99.01	0.95	0.95	2	-
GCF_001954275.1	s__Mycobacterium sp001954275	80.2917	846	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.75	98.75	0.90	0.90	2	-
GCF_001667035.1	s__Mycobacterium sp001667035	80.2868	881	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010730055.1	s__Mycobacterium shinjukuense	80.1094	705	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
GCF_001053185.1	s__Mycobacterium bohemicum	80.1056	823	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.81	99.81	0.97	0.97	2	-
GCF_003284935.1	s__Mycobacterium arosiense_A	80.0919	832	1511	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	79.7256	614	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001665875.1	s__Mycobacterium sp001665875	79.6939	840	1511	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	79.4654	773	1511	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	79.3177	749	1511	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.04	97.21	0.97	0.92	4	-
--------------------------------------------------------------------------------
[2024-01-24 11:07:17,327] [INFO] GTDB search result was written to GCF_002086415.1_ASM208641v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:07:17,328] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:07:17,331] [INFO] DFAST_QC result json was written to GCF_002086415.1_ASM208641v1_genomic.fna/dqc_result.json
[2024-01-24 11:07:17,332] [INFO] DFAST_QC completed!
[2024-01-24 11:07:17,332] [INFO] Total running time: 0h1m50s