[2024-01-24 13:36:59,708] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:36:59,710] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:36:59,711] [INFO] DQC Reference Directory: /var/lib/cwl/stg119acb85-a74c-48ab-a21b-f23fdad8c572/dqc_reference
[2024-01-24 13:37:00,976] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:37:00,976] [INFO] Task started: Prodigal
[2024-01-24 13:37:00,977] [INFO] Running command: gunzip -c /var/lib/cwl/stg32c2e8db-e963-495a-9c35-1b59ee66ebf3/GCF_012396015.1_ASM1239601v1_genomic.fna.gz | prodigal -d GCF_012396015.1_ASM1239601v1_genomic.fna/cds.fna -a GCF_012396015.1_ASM1239601v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:37:13,591] [INFO] Task succeeded: Prodigal
[2024-01-24 13:37:13,592] [INFO] Task started: HMMsearch
[2024-01-24 13:37:13,592] [INFO] Running command: hmmsearch --tblout GCF_012396015.1_ASM1239601v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg119acb85-a74c-48ab-a21b-f23fdad8c572/dqc_reference/reference_markers.hmm GCF_012396015.1_ASM1239601v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:37:13,941] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:37:13,943] [INFO] Found 6/6 markers.
[2024-01-24 13:37:13,982] [INFO] Query marker FASTA was written to GCF_012396015.1_ASM1239601v1_genomic.fna/markers.fasta
[2024-01-24 13:37:13,983] [INFO] Task started: Blastn
[2024-01-24 13:37:13,983] [INFO] Running command: blastn -query GCF_012396015.1_ASM1239601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119acb85-a74c-48ab-a21b-f23fdad8c572/dqc_reference/reference_markers.fasta -out GCF_012396015.1_ASM1239601v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:37:15,202] [INFO] Task succeeded: Blastn
[2024-01-24 13:37:15,205] [INFO] Selected 7 target genomes.
[2024-01-24 13:37:15,205] [INFO] Target genome list was writen to GCF_012396015.1_ASM1239601v1_genomic.fna/target_genomes.txt
[2024-01-24 13:37:15,209] [INFO] Task started: fastANI
[2024-01-24 13:37:15,209] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c2e8db-e963-495a-9c35-1b59ee66ebf3/GCF_012396015.1_ASM1239601v1_genomic.fna.gz --refList GCF_012396015.1_ASM1239601v1_genomic.fna/target_genomes.txt --output GCF_012396015.1_ASM1239601v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:37:23,593] [INFO] Task succeeded: fastANI
[2024-01-24 13:37:23,594] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg119acb85-a74c-48ab-a21b-f23fdad8c572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:37:23,594] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg119acb85-a74c-48ab-a21b-f23fdad8c572/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:37:23,602] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:37:23,602] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:37:23,602] [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
Tsukamurella spumae	strain=DSM 44113	GCA_012396015.1	44753	44753	type	True	100.0	1443	1448	95	conclusive
Tsukamurella pseudospumae	strain=JCM 13375	GCA_001575205.1	239498	239498	type	True	91.8713	1205	1448	95	below_threshold
Tsukamurella tyrosinosolvens	strain=NCTC13231	GCA_900637875.1	57704	57704	type	True	86.8741	1072	1448	95	below_threshold
Tsukamurella tyrosinosolvens	strain=CCUG 38499	GCA_001575155.1	57704	57704	type	True	86.832	1162	1448	95	below_threshold
Tsukamurella tyrosinosolvens	strain=DSM 44234	GCA_900104775.1	57704	57704	type	True	86.8195	1170	1448	95	below_threshold
Tsukamurella conjunctivitidis	strain=HKU72	GCA_007858475.1	2592068	2592068	type	True	86.3094	1151	1448	95	below_threshold
Tsukamurella asaccharolytica	strain=HKU71	GCA_007858435.1	2592067	2592067	type	True	85.7829	1014	1448	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:37:23,605] [INFO] DFAST Taxonomy check result was written to GCF_012396015.1_ASM1239601v1_genomic.fna/tc_result.tsv
[2024-01-24 13:37:23,608] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:37:23,609] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:37:23,609] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg119acb85-a74c-48ab-a21b-f23fdad8c572/dqc_reference/checkm_data
[2024-01-24 13:37:23,610] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:37:23,686] [INFO] Task started: CheckM
[2024-01-24 13:37:23,687] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_012396015.1_ASM1239601v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_012396015.1_ASM1239601v1_genomic.fna/checkm_input GCF_012396015.1_ASM1239601v1_genomic.fna/checkm_result
[2024-01-24 13:38:06,288] [INFO] Task succeeded: CheckM
[2024-01-24 13:38:06,290] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:38:06,313] [INFO] ===== Completeness check finished =====
[2024-01-24 13:38:06,313] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:38:06,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_012396015.1_ASM1239601v1_genomic.fna/markers.fasta)
[2024-01-24 13:38:06,314] [INFO] Task started: Blastn
[2024-01-24 13:38:06,315] [INFO] Running command: blastn -query GCF_012396015.1_ASM1239601v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg119acb85-a74c-48ab-a21b-f23fdad8c572/dqc_reference/reference_markers_gtdb.fasta -out GCF_012396015.1_ASM1239601v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:38:08,271] [INFO] Task succeeded: Blastn
[2024-01-24 13:38:08,275] [INFO] Selected 8 target genomes.
[2024-01-24 13:38:08,276] [INFO] Target genome list was writen to GCF_012396015.1_ASM1239601v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:38:08,286] [INFO] Task started: fastANI
[2024-01-24 13:38:08,287] [INFO] Running command: fastANI --query /var/lib/cwl/stg32c2e8db-e963-495a-9c35-1b59ee66ebf3/GCF_012396015.1_ASM1239601v1_genomic.fna.gz --refList GCF_012396015.1_ASM1239601v1_genomic.fna/target_genomes_gtdb.txt --output GCF_012396015.1_ASM1239601v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:38:18,541] [INFO] Task succeeded: fastANI
[2024-01-24 13:38:18,562] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:38:18,563] [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_012396015.1	s__Tsukamurella spumae	100.0	1443	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001575205.1	s__Tsukamurella pseudospumae	91.9055	1202	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	98.07	98.07	0.92	0.92	2	-
GCF_900104775.1	s__Tsukamurella tyrosinosolvens	86.8043	1172	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.14	98.76	0.95	0.91	8	-
GCF_007858445.1	s__Tsukamurella sputi	86.3223	1120	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858475.1	s__Tsukamurella conjunctivitidis	86.2787	1154	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.89	99.89	0.98	0.98	2	-
GCF_900631615.1	s__Tsukamurella paurometabola_A	86.2453	1103	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103175.1	s__Tsukamurella pulmonis	86.21	1097	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.49	98.89	0.96	0.93	5	-
GCF_007858435.1	s__Tsukamurella asaccharolytica	85.7718	1015	1448	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:38:18,565] [INFO] GTDB search result was written to GCF_012396015.1_ASM1239601v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:38:18,565] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:38:18,569] [INFO] DFAST_QC result json was written to GCF_012396015.1_ASM1239601v1_genomic.fna/dqc_result.json
[2024-01-24 13:38:18,569] [INFO] DFAST_QC completed!
[2024-01-24 13:38:18,569] [INFO] Total running time: 0h1m19s