[2024-01-25 19:33:35,946] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:33:35,947] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:33:35,947] [INFO] DQC Reference Directory: /var/lib/cwl/stg929e543f-c308-49fe-ba2c-f96be97c724d/dqc_reference
[2024-01-25 19:33:37,063] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:33:37,064] [INFO] Task started: Prodigal
[2024-01-25 19:33:37,064] [INFO] Running command: gunzip -c /var/lib/cwl/stga373921b-ac42-4d0d-bb5b-0f3d04f27d5b/GCF_900460355.1_51765_C02_genomic.fna.gz | prodigal -d GCF_900460355.1_51765_C02_genomic.fna/cds.fna -a GCF_900460355.1_51765_C02_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:33:50,972] [INFO] Task succeeded: Prodigal
[2024-01-25 19:33:50,972] [INFO] Task started: HMMsearch
[2024-01-25 19:33:50,973] [INFO] Running command: hmmsearch --tblout GCF_900460355.1_51765_C02_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg929e543f-c308-49fe-ba2c-f96be97c724d/dqc_reference/reference_markers.hmm GCF_900460355.1_51765_C02_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:33:51,175] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:33:51,177] [INFO] Found 6/6 markers.
[2024-01-25 19:33:51,219] [INFO] Query marker FASTA was written to GCF_900460355.1_51765_C02_genomic.fna/markers.fasta
[2024-01-25 19:33:51,220] [INFO] Task started: Blastn
[2024-01-25 19:33:51,220] [INFO] Running command: blastn -query GCF_900460355.1_51765_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg929e543f-c308-49fe-ba2c-f96be97c724d/dqc_reference/reference_markers.fasta -out GCF_900460355.1_51765_C02_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:33:52,400] [INFO] Task succeeded: Blastn
[2024-01-25 19:33:52,403] [INFO] Selected 9 target genomes.
[2024-01-25 19:33:52,404] [INFO] Target genome list was writen to GCF_900460355.1_51765_C02_genomic.fna/target_genomes.txt
[2024-01-25 19:33:52,408] [INFO] Task started: fastANI
[2024-01-25 19:33:52,408] [INFO] Running command: fastANI --query /var/lib/cwl/stga373921b-ac42-4d0d-bb5b-0f3d04f27d5b/GCF_900460355.1_51765_C02_genomic.fna.gz --refList GCF_900460355.1_51765_C02_genomic.fna/target_genomes.txt --output GCF_900460355.1_51765_C02_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:34:01,872] [INFO] Task succeeded: fastANI
[2024-01-25 19:34:01,873] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg929e543f-c308-49fe-ba2c-f96be97c724d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:34:01,873] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg929e543f-c308-49fe-ba2c-f96be97c724d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:34:01,880] [INFO] Found 9 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:34:01,880] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:34:01,881] [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 paurometabola	strain=NCTC13232	GCA_900460355.1	2061	2061	type	True	100.0	1492	1492	95	conclusive
Tsukamurella paurometabola	strain=DSM 20162	GCA_000092225.1	2061	2061	type	True	99.9997	1489	1492	95	conclusive
Tsukamurella tyrosinosolvens	strain=NCTC13231	GCA_900637875.1	57704	57704	type	True	83.2312	949	1492	95	below_threshold
Tsukamurella tyrosinosolvens	strain=DSM 44234	GCA_900104775.1	57704	57704	type	True	83.1199	1068	1492	95	below_threshold
Tsukamurella pulmonis	strain=NCTC13230	GCA_900460155.1	47312	47312	type	True	83.0899	1035	1492	95	below_threshold
Tsukamurella pulmonis	strain=DSM 44142	GCA_900103175.1	47312	47312	type	True	83.0372	1020	1492	95	below_threshold
Tsukamurella pulmonis	strain=CCUG 35732	GCA_001575165.1	47312	47312	type	True	83.0139	1033	1492	95	below_threshold
Tsukamurella conjunctivitidis	strain=HKU72	GCA_007858475.1	2592068	2592068	type	True	82.7955	1014	1492	95	below_threshold
Tsukamurella asaccharolytica	strain=HKU71	GCA_007858435.1	2592067	2592067	type	True	82.5768	913	1492	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:34:01,883] [INFO] DFAST Taxonomy check result was written to GCF_900460355.1_51765_C02_genomic.fna/tc_result.tsv
[2024-01-25 19:34:01,885] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:34:01,885] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:34:01,885] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg929e543f-c308-49fe-ba2c-f96be97c724d/dqc_reference/checkm_data
[2024-01-25 19:34:01,886] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:34:01,929] [INFO] Task started: CheckM
[2024-01-25 19:34:01,929] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460355.1_51765_C02_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460355.1_51765_C02_genomic.fna/checkm_input GCF_900460355.1_51765_C02_genomic.fna/checkm_result
[2024-01-25 19:34:49,192] [INFO] Task succeeded: CheckM
[2024-01-25 19:34:49,193] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:34:49,213] [INFO] ===== Completeness check finished =====
[2024-01-25 19:34:49,213] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:34:49,216] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460355.1_51765_C02_genomic.fna/markers.fasta)
[2024-01-25 19:34:49,216] [INFO] Task started: Blastn
[2024-01-25 19:34:49,216] [INFO] Running command: blastn -query GCF_900460355.1_51765_C02_genomic.fna/markers.fasta -db /var/lib/cwl/stg929e543f-c308-49fe-ba2c-f96be97c724d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460355.1_51765_C02_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:34:51,073] [INFO] Task succeeded: Blastn
[2024-01-25 19:34:51,077] [INFO] Selected 9 target genomes.
[2024-01-25 19:34:51,077] [INFO] Target genome list was writen to GCF_900460355.1_51765_C02_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:34:51,081] [INFO] Task started: fastANI
[2024-01-25 19:34:51,081] [INFO] Running command: fastANI --query /var/lib/cwl/stga373921b-ac42-4d0d-bb5b-0f3d04f27d5b/GCF_900460355.1_51765_C02_genomic.fna.gz --refList GCF_900460355.1_51765_C02_genomic.fna/target_genomes_gtdb.txt --output GCF_900460355.1_51765_C02_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:35:01,002] [INFO] Task succeeded: fastANI
[2024-01-25 19:35:01,008] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:35:01,009] [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_000092225.1	s__Tsukamurella paurometabola	99.9997	1488	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	100.00	100.00	1.00	1.00	2	conclusive
GCF_900104775.1	s__Tsukamurella tyrosinosolvens	83.1361	1067	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.14	98.76	0.95	0.91	8	-
GCF_900103175.1	s__Tsukamurella pulmonis	83.008	1021	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.49	98.89	0.96	0.93	5	-
GCF_900631615.1	s__Tsukamurella paurometabola_A	82.8947	1025	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858445.1	s__Tsukamurella sputi	82.84	1008	1492	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	82.8198	1011	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.89	99.89	0.98	0.98	2	-
GCF_007858435.1	s__Tsukamurella asaccharolytica	82.6229	909	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000312385.1	s__Tsukamurella sp000312385	82.6034	998	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_012396015.1	s__Tsukamurella spumae	82.4669	912	1492	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:35:01,011] [INFO] GTDB search result was written to GCF_900460355.1_51765_C02_genomic.fna/result_gtdb.tsv
[2024-01-25 19:35:01,011] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:35:01,014] [INFO] DFAST_QC result json was written to GCF_900460355.1_51765_C02_genomic.fna/dqc_result.json
[2024-01-25 19:35:01,015] [INFO] DFAST_QC completed!
[2024-01-25 19:35:01,015] [INFO] Total running time: 0h1m25s