[2024-01-25 19:11:35,403] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:11:35,404] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:11:35,404] [INFO] DQC Reference Directory: /var/lib/cwl/stge960c334-f768-4997-98c2-86c2d6532455/dqc_reference
[2024-01-25 19:11:36,513] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:11:36,514] [INFO] Task started: Prodigal
[2024-01-25 19:11:36,514] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a520ce8-89f8-4267-a32c-8d119f9486bd/GCF_025823245.1_ASM2582324v1_genomic.fna.gz | prodigal -d GCF_025823245.1_ASM2582324v1_genomic.fna/cds.fna -a GCF_025823245.1_ASM2582324v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:11:51,664] [INFO] Task succeeded: Prodigal
[2024-01-25 19:11:51,664] [INFO] Task started: HMMsearch
[2024-01-25 19:11:51,664] [INFO] Running command: hmmsearch --tblout GCF_025823245.1_ASM2582324v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge960c334-f768-4997-98c2-86c2d6532455/dqc_reference/reference_markers.hmm GCF_025823245.1_ASM2582324v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:11:51,975] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:11:51,976] [INFO] Found 6/6 markers.
[2024-01-25 19:11:52,030] [INFO] Query marker FASTA was written to GCF_025823245.1_ASM2582324v1_genomic.fna/markers.fasta
[2024-01-25 19:11:52,030] [INFO] Task started: Blastn
[2024-01-25 19:11:52,030] [INFO] Running command: blastn -query GCF_025823245.1_ASM2582324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge960c334-f768-4997-98c2-86c2d6532455/dqc_reference/reference_markers.fasta -out GCF_025823245.1_ASM2582324v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:11:53,153] [INFO] Task succeeded: Blastn
[2024-01-25 19:11:53,156] [INFO] Selected 14 target genomes.
[2024-01-25 19:11:53,156] [INFO] Target genome list was writen to GCF_025823245.1_ASM2582324v1_genomic.fna/target_genomes.txt
[2024-01-25 19:11:53,177] [INFO] Task started: fastANI
[2024-01-25 19:11:53,178] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a520ce8-89f8-4267-a32c-8d119f9486bd/GCF_025823245.1_ASM2582324v1_genomic.fna.gz --refList GCF_025823245.1_ASM2582324v1_genomic.fna/target_genomes.txt --output GCF_025823245.1_ASM2582324v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:12:09,100] [INFO] Task succeeded: fastANI
[2024-01-25 19:12:09,100] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge960c334-f768-4997-98c2-86c2d6532455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:12:09,101] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge960c334-f768-4997-98c2-86c2d6532455/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:12:09,110] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 19:12:09,111] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:12:09,111] [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 fragae	strain=DSM 45731	GCA_002102185.1	1260918	1260918	type	True	99.9872	1548	1570	95	conclusive
Mycobacterium celatum	strain=DSM 44243	GCA_002101595.1	28045	28045	type	True	82.9547	1095	1570	95	below_threshold
Mycobacterium kyorinense	strain=KUM060204T	GCA_000759695.1	487514	487514	type	True	82.9206	1082	1570	95	below_threshold
Mycobacterium kyorinense	strain=DSM 45166	GCA_002101735.1	487514	487514	type	True	82.9135	1094	1570	95	below_threshold
Mycobacterium branderi	strain=JCM 12687	GCA_010728725.1	43348	43348	type	True	82.8152	1131	1570	95	below_threshold
Mycobacterium branderi	strain=DSM 44624	GCA_002086575.1	43348	43348	type	True	82.7564	1117	1570	95	below_threshold
Mycobacterium noviomagense	strain=DSM 45145	GCA_002086415.1	459858	459858	type	True	81.1358	999	1570	95	below_threshold
Mycobacterium noviomagense	strain=JCM 16367	GCA_010731635.1	459858	459858	type	True	81.0737	1028	1570	95	below_threshold
Mycobacterium xenopi	strain=DSM 43995	GCA_002102015.1	1789	1789	type	True	80.8701	952	1570	95	below_threshold
Mycobacterium cookii	strain=JCM 12404	GCA_010727945.1	1775	1775	type	True	80.8079	1001	1570	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	80.5867	961	1570	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	80.5355	953	1570	95	below_threshold
Mycolicibacterium moriokaense	strain=JCM 6375	GCA_010726085.1	39691	39691	type	True	78.8474	644	1570	95	below_threshold
Mycolicibacterium moriokaense	strain=CIP105393	GCA_002086395.1	39691	39691	type	True	78.7595	629	1570	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:12:09,112] [INFO] DFAST Taxonomy check result was written to GCF_025823245.1_ASM2582324v1_genomic.fna/tc_result.tsv
[2024-01-25 19:12:09,113] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:12:09,113] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:12:09,113] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge960c334-f768-4997-98c2-86c2d6532455/dqc_reference/checkm_data
[2024-01-25 19:12:09,114] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:12:09,159] [INFO] Task started: CheckM
[2024-01-25 19:12:09,159] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823245.1_ASM2582324v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823245.1_ASM2582324v1_genomic.fna/checkm_input GCF_025823245.1_ASM2582324v1_genomic.fna/checkm_result
[2024-01-25 19:12:54,340] [INFO] Task succeeded: CheckM
[2024-01-25 19:12:54,341] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:12:54,364] [INFO] ===== Completeness check finished =====
[2024-01-25 19:12:54,364] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:12:54,364] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823245.1_ASM2582324v1_genomic.fna/markers.fasta)
[2024-01-25 19:12:54,365] [INFO] Task started: Blastn
[2024-01-25 19:12:54,365] [INFO] Running command: blastn -query GCF_025823245.1_ASM2582324v1_genomic.fna/markers.fasta -db /var/lib/cwl/stge960c334-f768-4997-98c2-86c2d6532455/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823245.1_ASM2582324v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:12:56,005] [INFO] Task succeeded: Blastn
[2024-01-25 19:12:56,008] [INFO] Selected 14 target genomes.
[2024-01-25 19:12:56,008] [INFO] Target genome list was writen to GCF_025823245.1_ASM2582324v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:12:56,035] [INFO] Task started: fastANI
[2024-01-25 19:12:56,035] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a520ce8-89f8-4267-a32c-8d119f9486bd/GCF_025823245.1_ASM2582324v1_genomic.fna.gz --refList GCF_025823245.1_ASM2582324v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823245.1_ASM2582324v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:13:13,400] [INFO] Task succeeded: fastANI
[2024-01-25 19:13:13,409] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:13:13,409] [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_002102185.1	s__Mycobacterium fragae	99.9872	1548	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_003402475.1	s__Mycobacterium sp003402475	83.1253	1129	1570	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	82.9702	1095	1570	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	82.9057	1096	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.84	99.84	0.96	0.94	3	-
GCF_010728725.1	s__Mycobacterium branderi	82.7907	1132	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCA_019236925.1	s__Mycobacterium sp019236925	82.1334	929	1570	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	81.8095	997	1570	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	81.5819	989	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.72	99.46	0.97	0.95	3	-
GCF_010731635.1	s__Mycobacterium noviomagense	81.0661	1029	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_010727945.1	s__Mycobacterium cookii	80.8042	1002	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002105755.1	s__Mycobacterium colombiense	80.5914	959	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_000277125.1	s__Mycobacterium intracellulare	80.5335	954	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.48	95.71	0.93	0.84	82	-
GCA_019246375.1	s__Mycobacterium sp019246375	80.4878	613	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726085.1	s__Mycobacterium moriokaense	78.8483	645	1570	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-25 19:13:13,411] [INFO] GTDB search result was written to GCF_025823245.1_ASM2582324v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:13:13,412] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:13:13,415] [INFO] DFAST_QC result json was written to GCF_025823245.1_ASM2582324v1_genomic.fna/dqc_result.json
[2024-01-25 19:13:13,415] [INFO] DFAST_QC completed!
[2024-01-25 19:13:13,415] [INFO] Total running time: 0h1m38s