[2024-01-24 14:14:37,213] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:14:37,219] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:14:37,220] [INFO] DQC Reference Directory: /var/lib/cwl/stg5236a6de-8ca0-4a96-a863-313eb3f0c00c/dqc_reference
[2024-01-24 14:14:38,819] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:14:38,825] [INFO] Task started: Prodigal
[2024-01-24 14:14:38,826] [INFO] Running command: gunzip -c /var/lib/cwl/stga4ddab15-2b8e-4c08-982b-b6948f2fd565/GCF_003584745.1_ASM358474v1_genomic.fna.gz | prodigal -d GCF_003584745.1_ASM358474v1_genomic.fna/cds.fna -a GCF_003584745.1_ASM358474v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:15:03,774] [INFO] Task succeeded: Prodigal
[2024-01-24 14:15:03,774] [INFO] Task started: HMMsearch
[2024-01-24 14:15:03,774] [INFO] Running command: hmmsearch --tblout GCF_003584745.1_ASM358474v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg5236a6de-8ca0-4a96-a863-313eb3f0c00c/dqc_reference/reference_markers.hmm GCF_003584745.1_ASM358474v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:15:04,084] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:15:04,085] [INFO] Found 6/6 markers.
[2024-01-24 14:15:04,144] [INFO] Query marker FASTA was written to GCF_003584745.1_ASM358474v1_genomic.fna/markers.fasta
[2024-01-24 14:15:04,145] [INFO] Task started: Blastn
[2024-01-24 14:15:04,145] [INFO] Running command: blastn -query GCF_003584745.1_ASM358474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5236a6de-8ca0-4a96-a863-313eb3f0c00c/dqc_reference/reference_markers.fasta -out GCF_003584745.1_ASM358474v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:15:05,274] [INFO] Task succeeded: Blastn
[2024-01-24 14:15:05,278] [INFO] Selected 6 target genomes.
[2024-01-24 14:15:05,278] [INFO] Target genome list was writen to GCF_003584745.1_ASM358474v1_genomic.fna/target_genomes.txt
[2024-01-24 14:15:05,288] [INFO] Task started: fastANI
[2024-01-24 14:15:05,288] [INFO] Running command: fastANI --query /var/lib/cwl/stga4ddab15-2b8e-4c08-982b-b6948f2fd565/GCF_003584745.1_ASM358474v1_genomic.fna.gz --refList GCF_003584745.1_ASM358474v1_genomic.fna/target_genomes.txt --output GCF_003584745.1_ASM358474v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:15:33,456] [INFO] Task succeeded: fastANI
[2024-01-24 14:15:33,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg5236a6de-8ca0-4a96-a863-313eb3f0c00c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:15:33,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg5236a6de-8ca0-4a96-a863-313eb3f0c00c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:15:33,503] [INFO] Found 6 fastANI hits (6 hits with ANI > threshold)
[2024-01-24 14:15:33,503] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 14:15:33,503] [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 pseudoshottsii	strain=JCM 15466	GCA_003584745.1	265949	265949	suspected-type	True	100.0	2020	2020	95	inconclusive
Mycobacterium pseudoshottsii	strain=JCM 15466	GCA_001515365.1	265949	265949	suspected-type	True	99.884	1830	2020	95	inconclusive
Mycobacterium marinum	strain=CCUG20998	GCA_003391395.1	1781	1781	suspected-type	True	98.0082	1878	2020	95	inconclusive
Mycobacterium marinum	strain=DSM 44344	GCA_003431645.1	1781	1781	suspected-type	True	97.9806	1863	2020	95	inconclusive
Mycobacterium marinum	strain=NCTC2275	GCA_003431655.1	1781	1781	suspected-type	True	97.9389	1851	2020	95	inconclusive
Mycobacterium shottsii	strain=JCM 12657	GCA_010728525.1	133549	133549	suspected-type	True	97.355	1764	2020	95	inconclusive
--------------------------------------------------------------------------------
[2024-01-24 14:15:33,505] [INFO] DFAST Taxonomy check result was written to GCF_003584745.1_ASM358474v1_genomic.fna/tc_result.tsv
[2024-01-24 14:15:33,505] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:15:33,505] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:15:33,506] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg5236a6de-8ca0-4a96-a863-313eb3f0c00c/dqc_reference/checkm_data
[2024-01-24 14:15:33,511] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:15:33,572] [INFO] Task started: CheckM
[2024-01-24 14:15:33,572] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003584745.1_ASM358474v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003584745.1_ASM358474v1_genomic.fna/checkm_input GCF_003584745.1_ASM358474v1_genomic.fna/checkm_result
[2024-01-24 14:16:46,455] [INFO] Task succeeded: CheckM
[2024-01-24 14:16:46,458] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:16:46,481] [INFO] ===== Completeness check finished =====
[2024-01-24 14:16:46,481] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:16:46,482] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003584745.1_ASM358474v1_genomic.fna/markers.fasta)
[2024-01-24 14:16:46,482] [INFO] Task started: Blastn
[2024-01-24 14:16:46,482] [INFO] Running command: blastn -query GCF_003584745.1_ASM358474v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg5236a6de-8ca0-4a96-a863-313eb3f0c00c/dqc_reference/reference_markers_gtdb.fasta -out GCF_003584745.1_ASM358474v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:16:49,130] [INFO] Task succeeded: Blastn
[2024-01-24 14:16:49,134] [INFO] Selected 18 target genomes.
[2024-01-24 14:16:49,135] [INFO] Target genome list was writen to GCF_003584745.1_ASM358474v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:16:49,166] [INFO] Task started: fastANI
[2024-01-24 14:16:49,167] [INFO] Running command: fastANI --query /var/lib/cwl/stga4ddab15-2b8e-4c08-982b-b6948f2fd565/GCF_003584745.1_ASM358474v1_genomic.fna.gz --refList GCF_003584745.1_ASM358474v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003584745.1_ASM358474v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:17:20,178] [INFO] Task succeeded: fastANI
[2024-01-24 14:17:20,256] [INFO] Found 18 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:17:20,256] [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_003391395.1	s__Mycobacterium marinum	98.0082	1878	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.78	97.50	0.95	0.86	40	conclusive
GCF_900566055.1	s__Mycobacterium innocens	81.1074	1146	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.27	98.57	0.94	0.90	3	-
GCF_900292015.1	s__Mycobacterium basiliense	80.9751	1272	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002705925.1	s__Mycobacterium ostraviense	80.9575	1220	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.87	99.87	0.99	0.99	2	-
GCF_002102175.1	s__Mycobacterium gastri	80.9354	1167	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.95	99.95	0.95	0.95	2	-
GCF_900566075.1	s__Mycobacterium pseudokansasii	80.9085	1185	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.70	99.48	0.96	0.94	7	-
GCF_002086675.1	s__Mycobacterium persicum	80.8085	1133	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.71	99.58	0.97	0.95	12	-
GCF_009741445.1	s__Mycobacterium avium	80.4182	930	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	96.9043	98.75	98.29	0.92	0.84	206	-
GCF_002086155.1	s__Mycobacterium angelicum	80.3024	1090	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104675.1	s__Mycobacterium decipiens	80.2172	1010	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002116635.1	s__Mycobacterium szulgai	80.1777	1101	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002102225.1	s__Mycobacterium interjectum_B	80.0959	1006	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001417955.2	s__Mycobacterium gordonae_B	80.0621	1011	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003614435.1	s__Mycobacterium paragordonae	79.9359	1045	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.23	97.83	0.93	0.88	9	-
GCF_015689175.1	s__Mycobacterium kubicae	79.8389	910	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.05	97.98	0.96	0.92	7	-
GCF_002101675.1	s__Mycobacterium gordonae	79.7907	1002	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.22	98.97	0.90	0.87	6	-
GCF_017086405.1	s__Mycobacterium gordonae_D	79.6884	1012	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010729105.1	s__Mycobacterium saskatchewanense	79.5062	923	2020	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.98	99.98	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:17:20,258] [INFO] GTDB search result was written to GCF_003584745.1_ASM358474v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:17:20,258] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:17:20,263] [INFO] DFAST_QC result json was written to GCF_003584745.1_ASM358474v1_genomic.fna/dqc_result.json
[2024-01-24 14:17:20,264] [INFO] DFAST_QC completed!
[2024-01-24 14:17:20,264] [INFO] Total running time: 0h2m43s