[2024-01-25 18:39:20,446] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:20,448] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:20,448] [INFO] DQC Reference Directory: /var/lib/cwl/stg8c349306-ae76-4b29-845d-5e69b0bd5b9a/dqc_reference
[2024-01-25 18:39:21,618] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:21,618] [INFO] Task started: Prodigal
[2024-01-25 18:39:21,619] [INFO] Running command: gunzip -c /var/lib/cwl/stg5c5cfdda-cebe-4616-bb45-22be0b2602ee/GCF_025822435.1_ASM2582243v1_genomic.fna.gz | prodigal -d GCF_025822435.1_ASM2582243v1_genomic.fna/cds.fna -a GCF_025822435.1_ASM2582243v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:39:38,335] [INFO] Task succeeded: Prodigal
[2024-01-25 18:39:38,335] [INFO] Task started: HMMsearch
[2024-01-25 18:39:38,336] [INFO] Running command: hmmsearch --tblout GCF_025822435.1_ASM2582243v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg8c349306-ae76-4b29-845d-5e69b0bd5b9a/dqc_reference/reference_markers.hmm GCF_025822435.1_ASM2582243v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:39:38,606] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:39:38,607] [INFO] Found 6/6 markers.
[2024-01-25 18:39:38,658] [INFO] Query marker FASTA was written to GCF_025822435.1_ASM2582243v1_genomic.fna/markers.fasta
[2024-01-25 18:39:38,658] [INFO] Task started: Blastn
[2024-01-25 18:39:38,658] [INFO] Running command: blastn -query GCF_025822435.1_ASM2582243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c349306-ae76-4b29-845d-5e69b0bd5b9a/dqc_reference/reference_markers.fasta -out GCF_025822435.1_ASM2582243v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:39:39,893] [INFO] Task succeeded: Blastn
[2024-01-25 18:39:39,895] [INFO] Selected 10 target genomes.
[2024-01-25 18:39:39,896] [INFO] Target genome list was writen to GCF_025822435.1_ASM2582243v1_genomic.fna/target_genomes.txt
[2024-01-25 18:39:39,904] [INFO] Task started: fastANI
[2024-01-25 18:39:39,904] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c5cfdda-cebe-4616-bb45-22be0b2602ee/GCF_025822435.1_ASM2582243v1_genomic.fna.gz --refList GCF_025822435.1_ASM2582243v1_genomic.fna/target_genomes.txt --output GCF_025822435.1_ASM2582243v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:39:54,443] [INFO] Task succeeded: fastANI
[2024-01-25 18:39:54,444] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg8c349306-ae76-4b29-845d-5e69b0bd5b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:39:54,444] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg8c349306-ae76-4b29-845d-5e69b0bd5b9a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:39:54,452] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 18:39:54,452] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-25 18:39:54,452] [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 crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	99.9949	1947	1950	95	inconclusive
Mycobacterium pallens	strain=JCM 16370	GCA_019456675.1	370524	370524	type	True	96.2927	1768	1950	95	inconclusive
Mycolicibacterium rhodesiae	strain=DSM 44223	GCA_002086695.1	36814	36814	type	True	86.9229	1575	1950	95	below_threshold
Mycolicibacterium aichiense	strain=JCM 6376	GCA_010726245.1	1799	1799	type	True	86.6298	1557	1950	95	below_threshold
Mycolicibacterium aichiense	strain=NCTC10820	GCA_900453085.1	1799	1799	type	True	86.6034	1567	1950	95	below_threshold
Mycolicibacterium aromaticivorans	strain=JS19b1	GCA_000559085.2	318425	318425	type	True	86.5612	1560	1950	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	84.7194	1481	1950	95	below_threshold
Mycolicibacterium helvum	strain=JCM 30396	GCA_010731895.1	1534349	1534349	type	True	84.1637	1406	1950	95	below_threshold
Mycolicibacterium anyangense	strain=JCM 30275	GCA_010731855.1	1431246	1431246	type	True	81.9835	1102	1950	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	79.3914	876	1950	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:39:54,456] [INFO] DFAST Taxonomy check result was written to GCF_025822435.1_ASM2582243v1_genomic.fna/tc_result.tsv
[2024-01-25 18:39:54,457] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:39:54,457] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:39:54,457] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg8c349306-ae76-4b29-845d-5e69b0bd5b9a/dqc_reference/checkm_data
[2024-01-25 18:39:54,458] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:39:54,514] [INFO] Task started: CheckM
[2024-01-25 18:39:54,514] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025822435.1_ASM2582243v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025822435.1_ASM2582243v1_genomic.fna/checkm_input GCF_025822435.1_ASM2582243v1_genomic.fna/checkm_result
[2024-01-25 18:40:47,525] [INFO] Task succeeded: CheckM
[2024-01-25 18:40:47,527] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:40:47,545] [INFO] ===== Completeness check finished =====
[2024-01-25 18:40:47,546] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:40:47,546] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025822435.1_ASM2582243v1_genomic.fna/markers.fasta)
[2024-01-25 18:40:47,547] [INFO] Task started: Blastn
[2024-01-25 18:40:47,547] [INFO] Running command: blastn -query GCF_025822435.1_ASM2582243v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg8c349306-ae76-4b29-845d-5e69b0bd5b9a/dqc_reference/reference_markers_gtdb.fasta -out GCF_025822435.1_ASM2582243v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:49,696] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:49,701] [INFO] Selected 10 target genomes.
[2024-01-25 18:40:49,701] [INFO] Target genome list was writen to GCF_025822435.1_ASM2582243v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:40:49,707] [INFO] Task started: fastANI
[2024-01-25 18:40:49,707] [INFO] Running command: fastANI --query /var/lib/cwl/stg5c5cfdda-cebe-4616-bb45-22be0b2602ee/GCF_025822435.1_ASM2582243v1_genomic.fna.gz --refList GCF_025822435.1_ASM2582243v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025822435.1_ASM2582243v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:41:05,162] [INFO] Task succeeded: fastANI
[2024-01-25 18:41:05,170] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:41:05,170] [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_001886515.1	s__Mycobacterium sp001886515	96.3426	1758	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.54	98.54	0.94	0.94	2	conclusive
GCF_001021385.1	s__Mycobacterium sp001021385	88.2114	1650	1950	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	87.4932	1489	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002086695.1	s__Mycobacterium rhodesiae	86.9292	1575	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008329905.1	s__Mycobacterium sp008329905	86.7616	1599	1950	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	86.6682	1534	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010726245.1	s__Mycobacterium aichiense	86.6199	1560	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000559085.1	s__Mycobacterium aromaticivorans	86.563	1561	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_900078375.1	s__Mycobacterium sp900078375	84.6742	1461	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002007745.1	s__Mycobacterium litorale_A	82.6912	1256	1950	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:41:05,172] [INFO] GTDB search result was written to GCF_025822435.1_ASM2582243v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:41:05,172] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:41:05,175] [INFO] DFAST_QC result json was written to GCF_025822435.1_ASM2582243v1_genomic.fna/dqc_result.json
[2024-01-25 18:41:05,175] [INFO] DFAST_QC completed!
[2024-01-25 18:41:05,175] [INFO] Total running time: 0h1m45s