[2024-01-24 15:26:33,177] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:26:33,179] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:26:33,179] [INFO] DQC Reference Directory: /var/lib/cwl/stg158c790a-b21a-420a-b9ed-45b77154e6c8/dqc_reference
[2024-01-24 15:26:34,442] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:26:34,442] [INFO] Task started: Prodigal
[2024-01-24 15:26:34,443] [INFO] Running command: gunzip -c /var/lib/cwl/stgdbc2fc30-b6a0-439c-8f55-7787264a67aa/GCF_019668465.1_ASM1966846v1_genomic.fna.gz | prodigal -d GCF_019668465.1_ASM1966846v1_genomic.fna/cds.fna -a GCF_019668465.1_ASM1966846v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:27:04,702] [INFO] Task succeeded: Prodigal
[2024-01-24 15:27:04,703] [INFO] Task started: HMMsearch
[2024-01-24 15:27:04,703] [INFO] Running command: hmmsearch --tblout GCF_019668465.1_ASM1966846v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg158c790a-b21a-420a-b9ed-45b77154e6c8/dqc_reference/reference_markers.hmm GCF_019668465.1_ASM1966846v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:27:05,048] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:27:05,049] [INFO] Found 6/6 markers.
[2024-01-24 15:27:05,113] [INFO] Query marker FASTA was written to GCF_019668465.1_ASM1966846v1_genomic.fna/markers.fasta
[2024-01-24 15:27:05,114] [INFO] Task started: Blastn
[2024-01-24 15:27:05,114] [INFO] Running command: blastn -query GCF_019668465.1_ASM1966846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg158c790a-b21a-420a-b9ed-45b77154e6c8/dqc_reference/reference_markers.fasta -out GCF_019668465.1_ASM1966846v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:27:06,405] [INFO] Task succeeded: Blastn
[2024-01-24 15:27:06,409] [INFO] Selected 8 target genomes.
[2024-01-24 15:27:06,410] [INFO] Target genome list was writen to GCF_019668465.1_ASM1966846v1_genomic.fna/target_genomes.txt
[2024-01-24 15:27:06,415] [INFO] Task started: fastANI
[2024-01-24 15:27:06,416] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc2fc30-b6a0-439c-8f55-7787264a67aa/GCF_019668465.1_ASM1966846v1_genomic.fna.gz --refList GCF_019668465.1_ASM1966846v1_genomic.fna/target_genomes.txt --output GCF_019668465.1_ASM1966846v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:27:18,328] [INFO] Task succeeded: fastANI
[2024-01-24 15:27:18,328] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg158c790a-b21a-420a-b9ed-45b77154e6c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:27:18,329] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg158c790a-b21a-420a-b9ed-45b77154e6c8/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:27:18,341] [INFO] Found 8 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 15:27:18,341] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 15:27:18,341] [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 colombiense	strain=CECT 3035	GCA_002105755.1	339268	339268	suspected-type	True	91.979	1556	1942	95	below_threshold
Mycobacterium colombiense	strain=CECT 3035	GCA_000222105.4	339268	339268	suspected-type	True	91.9536	1563	1942	95	below_threshold
Mycobacterium mantenii	strain=DSM 45255	GCA_002086335.1	560555	560555	type	True	89.3861	1582	1942	95	below_threshold
Mycobacterium mantenii	strain=JCM 18113	GCA_010731775.1	560555	560555	type	True	89.3657	1616	1942	95	below_threshold
Mycobacterium arosiense	strain=DSM 45069	GCA_002086125.1	425468	425468	type	True	88.7338	1417	1942	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_000277125.1	1767	1767	suspected-type	True	87.1068	1529	1942	95	below_threshold
Mycobacterium intracellulare	strain=ATCC 13950	GCA_023278525.1	1767	1767	suspected-type	True	87.1041	1532	1942	95	below_threshold
Mycobacterium paraintracellulare	strain=JCM 30622	GCA_010731935.1	1138383	1138383	suspected-type	True	86.947	1503	1942	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:27:18,344] [INFO] DFAST Taxonomy check result was written to GCF_019668465.1_ASM1966846v1_genomic.fna/tc_result.tsv
[2024-01-24 15:27:18,345] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:27:18,345] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:27:18,345] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg158c790a-b21a-420a-b9ed-45b77154e6c8/dqc_reference/checkm_data
[2024-01-24 15:27:18,347] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:27:18,402] [INFO] Task started: CheckM
[2024-01-24 15:27:18,402] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019668465.1_ASM1966846v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019668465.1_ASM1966846v1_genomic.fna/checkm_input GCF_019668465.1_ASM1966846v1_genomic.fna/checkm_result
[2024-01-24 15:28:44,299] [INFO] Task succeeded: CheckM
[2024-01-24 15:28:44,300] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 15:28:44,325] [INFO] ===== Completeness check finished =====
[2024-01-24 15:28:44,326] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:28:44,326] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019668465.1_ASM1966846v1_genomic.fna/markers.fasta)
[2024-01-24 15:28:44,327] [INFO] Task started: Blastn
[2024-01-24 15:28:44,327] [INFO] Running command: blastn -query GCF_019668465.1_ASM1966846v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg158c790a-b21a-420a-b9ed-45b77154e6c8/dqc_reference/reference_markers_gtdb.fasta -out GCF_019668465.1_ASM1966846v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:28:46,201] [INFO] Task succeeded: Blastn
[2024-01-24 15:28:46,204] [INFO] Selected 7 target genomes.
[2024-01-24 15:28:46,205] [INFO] Target genome list was writen to GCF_019668465.1_ASM1966846v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:28:46,211] [INFO] Task started: fastANI
[2024-01-24 15:28:46,211] [INFO] Running command: fastANI --query /var/lib/cwl/stgdbc2fc30-b6a0-439c-8f55-7787264a67aa/GCF_019668465.1_ASM1966846v1_genomic.fna.gz --refList GCF_019668465.1_ASM1966846v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019668465.1_ASM1966846v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:28:57,155] [INFO] Task succeeded: fastANI
[2024-01-24 15:28:57,168] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2024-01-24 15:28:57,168] [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_001665835.1	s__Mycobacterium colombiense_A	93.4784	1591	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001672755.1	s__Mycobacterium colombiense_C	93.4047	1532	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002104765.1	s__Mycobacterium vulneris	93.3984	1652	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953985.1	s__Mycobacterium colombiense_B	93.3106	1579	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	97.54	96.91	0.93	0.88	12	-
GCF_002105755.1	s__Mycobacterium colombiense	91.9933	1554	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.60	97.75	0.94	0.91	4	-
GCF_010731775.1	s__Mycobacterium mantenii	89.3737	1614	1942	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	96.19	95.22	0.92	0.90	6	-
GCF_003284935.1	s__Mycobacterium arosiense_A	89.1759	1433	1942	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 15:28:57,172] [INFO] GTDB search result was written to GCF_019668465.1_ASM1966846v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:28:57,172] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:28:57,175] [INFO] DFAST_QC result json was written to GCF_019668465.1_ASM1966846v1_genomic.fna/dqc_result.json
[2024-01-24 15:28:57,175] [INFO] DFAST_QC completed!
[2024-01-24 15:28:57,176] [INFO] Total running time: 0h2m24s