[2024-01-25 17:39:35,434] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:39:35,435] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:39:35,435] [INFO] DQC Reference Directory: /var/lib/cwl/stg0dc88cc2-52d6-4117-810f-3a924a01bb37/dqc_reference
[2024-01-25 17:39:36,566] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:39:36,567] [INFO] Task started: Prodigal
[2024-01-25 17:39:36,567] [INFO] Running command: gunzip -c /var/lib/cwl/stgb245338f-71ba-4cf7-ab05-bfdc8ef7097c/GCF_025823345.1_ASM2582334v1_genomic.fna.gz | prodigal -d GCF_025823345.1_ASM2582334v1_genomic.fna/cds.fna -a GCF_025823345.1_ASM2582334v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:39:51,618] [INFO] Task succeeded: Prodigal
[2024-01-25 17:39:51,618] [INFO] Task started: HMMsearch
[2024-01-25 17:39:51,619] [INFO] Running command: hmmsearch --tblout GCF_025823345.1_ASM2582334v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg0dc88cc2-52d6-4117-810f-3a924a01bb37/dqc_reference/reference_markers.hmm GCF_025823345.1_ASM2582334v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:39:51,921] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:39:51,922] [INFO] Found 6/6 markers.
[2024-01-25 17:39:51,968] [INFO] Query marker FASTA was written to GCF_025823345.1_ASM2582334v1_genomic.fna/markers.fasta
[2024-01-25 17:39:51,968] [INFO] Task started: Blastn
[2024-01-25 17:39:51,969] [INFO] Running command: blastn -query GCF_025823345.1_ASM2582334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc88cc2-52d6-4117-810f-3a924a01bb37/dqc_reference/reference_markers.fasta -out GCF_025823345.1_ASM2582334v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:39:53,238] [INFO] Task succeeded: Blastn
[2024-01-25 17:39:53,242] [INFO] Selected 10 target genomes.
[2024-01-25 17:39:53,242] [INFO] Target genome list was writen to GCF_025823345.1_ASM2582334v1_genomic.fna/target_genomes.txt
[2024-01-25 17:39:53,250] [INFO] Task started: fastANI
[2024-01-25 17:39:53,250] [INFO] Running command: fastANI --query /var/lib/cwl/stgb245338f-71ba-4cf7-ab05-bfdc8ef7097c/GCF_025823345.1_ASM2582334v1_genomic.fna.gz --refList GCF_025823345.1_ASM2582334v1_genomic.fna/target_genomes.txt --output GCF_025823345.1_ASM2582334v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:40:07,523] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:07,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg0dc88cc2-52d6-4117-810f-3a924a01bb37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:40:07,524] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg0dc88cc2-52d6-4117-810f-3a924a01bb37/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:40:07,533] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 17:40:07,533] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:40:07,533] [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 litorale	strain=JCM 17423	GCA_010731695.1	758802	758802	type	True	99.9973	1847	1848	95	conclusive
Mycolicibacterium litorale	strain=CGMCC 4.5724	GCA_004366555.1	758802	758802	type	True	99.9918	1841	1848	95	conclusive
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_014893035.1	2761578	2761578	type	True	87.4034	1489	1848	95	below_threshold
Mycolicibacterium baixiangningiae	strain=LJ126	GCA_016313185.1	2761578	2761578	type	True	87.3818	1484	1848	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_002086655.1	85693	85693	type	True	86.8404	1436	1848	95	below_threshold
Mycolicibacterium monacense	strain=DSM 44395	GCA_009931355.1	85693	85693	type	True	86.8176	1464	1848	95	below_threshold
Mycolicibacterium monacense	strain=JCM 15658	GCA_010731575.1	85693	85693	type	True	86.7585	1480	1848	95	below_threshold
Mycolicibacterium fortuitum subsp. fortuitum	strain=JCM 6387	GCA_022179545.1	144549	1766	type	True	80.2451	960	1848	95	below_threshold
Mycobacterium crocinum	strain=JCM 16369	GCA_022370635.3	388459	388459	type	True	79.9858	907	1848	95	below_threshold
Mycolicibacterium vinylchloridicum	strain=CECT 8761	GCA_013404075.1	2736928	2736928	type	True	79.8332	886	1848	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:40:07,534] [INFO] DFAST Taxonomy check result was written to GCF_025823345.1_ASM2582334v1_genomic.fna/tc_result.tsv
[2024-01-25 17:40:07,535] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:40:07,535] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:40:07,535] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg0dc88cc2-52d6-4117-810f-3a924a01bb37/dqc_reference/checkm_data
[2024-01-25 17:40:07,536] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:40:07,588] [INFO] Task started: CheckM
[2024-01-25 17:40:07,588] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_025823345.1_ASM2582334v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_025823345.1_ASM2582334v1_genomic.fna/checkm_input GCF_025823345.1_ASM2582334v1_genomic.fna/checkm_result
[2024-01-25 17:41:17,942] [INFO] Task succeeded: CheckM
[2024-01-25 17:41:17,943] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:41:17,960] [INFO] ===== Completeness check finished =====
[2024-01-25 17:41:17,961] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:41:17,961] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_025823345.1_ASM2582334v1_genomic.fna/markers.fasta)
[2024-01-25 17:41:17,962] [INFO] Task started: Blastn
[2024-01-25 17:41:17,962] [INFO] Running command: blastn -query GCF_025823345.1_ASM2582334v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg0dc88cc2-52d6-4117-810f-3a924a01bb37/dqc_reference/reference_markers_gtdb.fasta -out GCF_025823345.1_ASM2582334v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:41:20,157] [INFO] Task succeeded: Blastn
[2024-01-25 17:41:20,160] [INFO] Selected 12 target genomes.
[2024-01-25 17:41:20,160] [INFO] Target genome list was writen to GCF_025823345.1_ASM2582334v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:41:20,169] [INFO] Task started: fastANI
[2024-01-25 17:41:20,169] [INFO] Running command: fastANI --query /var/lib/cwl/stgb245338f-71ba-4cf7-ab05-bfdc8ef7097c/GCF_025823345.1_ASM2582334v1_genomic.fna.gz --refList GCF_025823345.1_ASM2582334v1_genomic.fna/target_genomes_gtdb.txt --output GCF_025823345.1_ASM2582334v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:41:37,332] [INFO] Task succeeded: fastANI
[2024-01-25 17:41:37,340] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:41:37,340] [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_010731695.1	s__Mycobacterium litorale	99.9973	1847	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_014218295.1	s__Mycobacterium litorale_B	88.112	1557	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016313185.1	s__Mycobacterium sp016313185	87.3732	1485	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.68	97.36	0.93	0.85	3	-
GCF_001499995.1	s__Mycobacterium sp001499995	86.9578	1403	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001500125.1	s__Mycobacterium sp001500125	86.8666	1446	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010731575.1	s__Mycobacterium monacense	86.7817	1477	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.29	98.82	0.95	0.89	9	-
GCF_004570325.1	s__Mycobacterium sp004570325	84.2509	1331	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017352375.1	s__Mycobacterium sp017352375	82.7967	1272	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000612725.1	s__Mycobacterium austroafricanum	81.3623	1092	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	98.53	98.42	0.88	0.88	3	-
GCF_002086815.1	s__Mycobacterium parafortuitum	81.1041	1118	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	100.00	100.00	1.00	1.00	2	-
GCF_900603025.1	s__Mycobacterium hassiacum	80.9286	990	1848	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Mycobacterium	95.0	99.99	99.99	1.00	1.00	3	-
GCF_001494595.1	s__Mycobacterium sp001494595	80.4495	906	1848	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 17:41:37,342] [INFO] GTDB search result was written to GCF_025823345.1_ASM2582334v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:41:37,342] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:41:37,345] [INFO] DFAST_QC result json was written to GCF_025823345.1_ASM2582334v1_genomic.fna/dqc_result.json
[2024-01-25 17:41:37,345] [INFO] DFAST_QC completed!
[2024-01-25 17:41:37,345] [INFO] Total running time: 0h2m2s