[2024-01-24 15:10:23,183] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:10:23,204] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:10:23,205] [INFO] DQC Reference Directory: /var/lib/cwl/stg58daed82-9fcb-471b-b16d-8c6a08f912a3/dqc_reference
[2024-01-24 15:10:24,725] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:10:24,725] [INFO] Task started: Prodigal
[2024-01-24 15:10:24,726] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0c904ef-b440-4199-a7ce-8d0712ef9f8f/GCF_002250655.1_ASM225065v1_genomic.fna.gz | prodigal -d GCF_002250655.1_ASM225065v1_genomic.fna/cds.fna -a GCF_002250655.1_ASM225065v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:10:45,103] [INFO] Task succeeded: Prodigal
[2024-01-24 15:10:45,103] [INFO] Task started: HMMsearch
[2024-01-24 15:10:45,103] [INFO] Running command: hmmsearch --tblout GCF_002250655.1_ASM225065v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg58daed82-9fcb-471b-b16d-8c6a08f912a3/dqc_reference/reference_markers.hmm GCF_002250655.1_ASM225065v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:10:45,437] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:10:45,439] [INFO] Found 6/6 markers.
[2024-01-24 15:10:45,489] [INFO] Query marker FASTA was written to GCF_002250655.1_ASM225065v1_genomic.fna/markers.fasta
[2024-01-24 15:10:45,489] [INFO] Task started: Blastn
[2024-01-24 15:10:45,489] [INFO] Running command: blastn -query GCF_002250655.1_ASM225065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58daed82-9fcb-471b-b16d-8c6a08f912a3/dqc_reference/reference_markers.fasta -out GCF_002250655.1_ASM225065v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:10:46,730] [INFO] Task succeeded: Blastn
[2024-01-24 15:10:46,734] [INFO] Selected 18 target genomes.
[2024-01-24 15:10:46,734] [INFO] Target genome list was writen to GCF_002250655.1_ASM225065v1_genomic.fna/target_genomes.txt
[2024-01-24 15:10:46,742] [INFO] Task started: fastANI
[2024-01-24 15:10:46,742] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0c904ef-b440-4199-a7ce-8d0712ef9f8f/GCF_002250655.1_ASM225065v1_genomic.fna.gz --refList GCF_002250655.1_ASM225065v1_genomic.fna/target_genomes.txt --output GCF_002250655.1_ASM225065v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:11:10,773] [INFO] Task succeeded: fastANI
[2024-01-24 15:11:10,774] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg58daed82-9fcb-471b-b16d-8c6a08f912a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:11:10,774] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg58daed82-9fcb-471b-b16d-8c6a08f912a3/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:11:10,788] [INFO] Found 17 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 15:11:10,789] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 15:11:10,789] [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
Mycolicibacterium sphagni	strain=ATCC 33027	GCA_002250655.1	1786	1786	type	True	100.0	1988	1992	95	conclusive
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	85.58	1477	1992	95	below_threshold
Mycolicibacterium sarraceniae	strain=JCM 30395	GCA_010731875.1	1534348	1534348	type	True	85.2418	1256	1992	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	84.8855	1430	1992	95	below_threshold
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	84.2683	1361	1992	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	84.084	1371	1992	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	83.7993	1387	1992	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	83.7953	1400	1992	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	81.5838	1110	1992	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.2943	784	1992	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	79.2655	791	1992	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	79.206	795	1992	95	below_threshold
Mycolicibacterium llatzerense	strain=MG13	GCA_025331195.1	280871	280871	type	True	79.1495	746	1992	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP3836	GCA_017724035.1	359387	456327	pathovar	True	74.9705	56	1992	95	below_threshold
Xanthomonas euvesicatoria pv. alfalfae	strain=CFBP 3836	GCA_000488955.1	359387	456327	pathovar	True	74.9705	56	1992	95	below_threshold
Xanthomonas citri	strain=CFBP7112	GCA_002218265.1	346	346	pathovar	True	74.9371	56	1992	95	below_threshold
Xanthomonas euvesicatoria	strain=ATCC 11633	GCA_020880415.1	456327	456327	type	True	74.8577	57	1992	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:11:10,791] [INFO] DFAST Taxonomy check result was written to GCF_002250655.1_ASM225065v1_genomic.fna/tc_result.tsv
[2024-01-24 15:11:10,792] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:11:10,792] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:11:10,792] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg58daed82-9fcb-471b-b16d-8c6a08f912a3/dqc_reference/checkm_data
[2024-01-24 15:11:10,794] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:11:10,849] [INFO] Task started: CheckM
[2024-01-24 15:11:10,850] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_002250655.1_ASM225065v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_002250655.1_ASM225065v1_genomic.fna/checkm_input GCF_002250655.1_ASM225065v1_genomic.fna/checkm_result
[2024-01-24 15:12:07,873] [INFO] Task succeeded: CheckM
[2024-01-24 15:12:07,874] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:12:07,892] [INFO] ===== Completeness check finished =====
[2024-01-24 15:12:07,893] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:12:07,893] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_002250655.1_ASM225065v1_genomic.fna/markers.fasta)
[2024-01-24 15:12:07,893] [INFO] Task started: Blastn
[2024-01-24 15:12:07,893] [INFO] Running command: blastn -query GCF_002250655.1_ASM225065v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg58daed82-9fcb-471b-b16d-8c6a08f912a3/dqc_reference/reference_markers_gtdb.fasta -out GCF_002250655.1_ASM225065v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:12:09,500] [INFO] Task succeeded: Blastn
[2024-01-24 15:12:09,504] [INFO] Selected 20 target genomes.
[2024-01-24 15:12:09,504] [INFO] Target genome list was writen to GCF_002250655.1_ASM225065v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:12:09,516] [INFO] Task started: fastANI
[2024-01-24 15:12:09,516] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0c904ef-b440-4199-a7ce-8d0712ef9f8f/GCF_002250655.1_ASM225065v1_genomic.fna.gz --refList GCF_002250655.1_ASM225065v1_genomic.fna/target_genomes_gtdb.txt --output GCF_002250655.1_ASM225065v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:12:34,944] [INFO] Task succeeded: fastANI
[2024-01-24 15:12:34,958] [INFO] Found 16 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:12:34,958] [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_002250655.1	s__Mycobacterium sphagni	100.0	1988	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_900078375.1	s__Mycobacterium sp900078375	86.1337	1475	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013337765.1	s__Mycobacterium sp003053865	85.9938	1481	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.43	95.41	0.83	0.83	3	-
GCF_010731895.1	s__Mycobacterium helvum	85.5777	1478	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731875.1	s__Mycobacterium sarraceniae	85.2334	1257	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004362315.1	s__Mycobacterium sp004362315	85.1874	1482	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.02	98.99	0.96	0.96	6	-
GCF_013404075.1	s__Mycobacterium sp013404075	84.8728	1432	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886515.1	s__Mycobacterium sp001886515	84.376	1344	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	-
GCF_008329905.1	s__Mycobacterium sp008329905	83.9649	1436	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002887815.1	s__Mycobacterium sp002887815	83.9027	1374	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001021385.1	s__Mycobacterium sp001021385	83.8138	1401	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329565.1	s__Mycobacterium sp008329565	83.586	1338	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001426545.1	s__Mycobacterium sp001426545	78.8256	765	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002043095.1	s__Mycobacterium sp002043095	78.7633	765	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	95.25	95.25	0.79	0.79	2	-
GCA_002863225.1	s__Mycobacterium sp002863225	78.7012	691	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_006439015.1	s__Mycobacterium hodleri_A	78.5552	693	1992	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 15:12:34,960] [INFO] GTDB search result was written to GCF_002250655.1_ASM225065v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:12:34,961] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:12:34,965] [INFO] DFAST_QC result json was written to GCF_002250655.1_ASM225065v1_genomic.fna/dqc_result.json
[2024-01-24 15:12:34,966] [INFO] DFAST_QC completed!
[2024-01-24 15:12:34,966] [INFO] Total running time: 0h2m12s