[2024-01-25 18:54:35,575] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:54:35,576] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:54:35,576] [INFO] DQC Reference Directory: /var/lib/cwl/stg23223516-bf0b-438e-a657-0ce2bcac2a8d/dqc_reference
[2024-01-25 18:54:36,752] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:54:36,753] [INFO] Task started: Prodigal
[2024-01-25 18:54:36,753] [INFO] Running command: gunzip -c /var/lib/cwl/stg93fd7127-77a2-438e-ad4b-44b32546f24b/GCF_900460155.1_52700_E01_genomic.fna.gz | prodigal -d GCF_900460155.1_52700_E01_genomic.fna/cds.fna -a GCF_900460155.1_52700_E01_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:54:49,622] [INFO] Task succeeded: Prodigal
[2024-01-25 18:54:49,622] [INFO] Task started: HMMsearch
[2024-01-25 18:54:49,622] [INFO] Running command: hmmsearch --tblout GCF_900460155.1_52700_E01_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg23223516-bf0b-438e-a657-0ce2bcac2a8d/dqc_reference/reference_markers.hmm GCF_900460155.1_52700_E01_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:54:49,902] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:54:49,902] [INFO] Found 6/6 markers.
[2024-01-25 18:54:49,942] [INFO] Query marker FASTA was written to GCF_900460155.1_52700_E01_genomic.fna/markers.fasta
[2024-01-25 18:54:49,942] [INFO] Task started: Blastn
[2024-01-25 18:54:49,942] [INFO] Running command: blastn -query GCF_900460155.1_52700_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg23223516-bf0b-438e-a657-0ce2bcac2a8d/dqc_reference/reference_markers.fasta -out GCF_900460155.1_52700_E01_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:54:51,213] [INFO] Task succeeded: Blastn
[2024-01-25 18:54:51,216] [INFO] Selected 9 target genomes.
[2024-01-25 18:54:51,216] [INFO] Target genome list was writen to GCF_900460155.1_52700_E01_genomic.fna/target_genomes.txt
[2024-01-25 18:54:51,270] [INFO] Task started: fastANI
[2024-01-25 18:54:51,270] [INFO] Running command: fastANI --query /var/lib/cwl/stg93fd7127-77a2-438e-ad4b-44b32546f24b/GCF_900460155.1_52700_E01_genomic.fna.gz --refList GCF_900460155.1_52700_E01_genomic.fna/target_genomes.txt --output GCF_900460155.1_52700_E01_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:55:02,824] [INFO] Task succeeded: fastANI
[2024-01-25 18:55:02,825] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg23223516-bf0b-438e-a657-0ce2bcac2a8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:55:02,825] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg23223516-bf0b-438e-a657-0ce2bcac2a8d/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:55:02,832] [INFO] Found 9 fastANI hits (3 hits with ANI > threshold)
[2024-01-25 18:55:02,832] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:55:02,832] [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 pulmonis	strain=NCTC13230	GCA_900460155.1	47312	47312	type	True	100.0	1587	1591	95	conclusive
Tsukamurella pulmonis	strain=DSM 44142	GCA_900103175.1	47312	47312	type	True	99.9993	1583	1591	95	conclusive
Tsukamurella pulmonis	strain=CCUG 35732	GCA_001575165.1	47312	47312	type	True	99.9956	1556	1591	95	conclusive
Tsukamurella tyrosinosolvens	strain=DSM 44234	GCA_900104775.1	57704	57704	type	True	88.8875	1315	1591	95	below_threshold
Tsukamurella tyrosinosolvens	strain=NCTC13231	GCA_900637875.1	57704	57704	type	True	88.8226	1213	1591	95	below_threshold
Tsukamurella conjunctivitidis	strain=HKU72	GCA_007858475.1	2592068	2592068	type	True	88.3939	1273	1591	95	below_threshold
Tsukamurella sputi	strain=HKU70	GCA_007858445.1	2591848	2591848	type	True	88.1969	1227	1591	95	below_threshold
Tsukamurella asaccharolytica	strain=HKU71	GCA_007858435.1	2592067	2592067	type	True	87.7286	1098	1591	95	below_threshold
Tsukamurella pseudospumae	strain=JCM 13375	GCA_001575205.1	239498	239498	type	True	86.2894	1218	1591	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:55:02,833] [INFO] DFAST Taxonomy check result was written to GCF_900460155.1_52700_E01_genomic.fna/tc_result.tsv
[2024-01-25 18:55:02,834] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:55:02,834] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:55:02,834] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg23223516-bf0b-438e-a657-0ce2bcac2a8d/dqc_reference/checkm_data
[2024-01-25 18:55:02,835] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:55:02,879] [INFO] Task started: CheckM
[2024-01-25 18:55:02,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900460155.1_52700_E01_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900460155.1_52700_E01_genomic.fna/checkm_input GCF_900460155.1_52700_E01_genomic.fna/checkm_result
[2024-01-25 18:56:06,893] [INFO] Task succeeded: CheckM
[2024-01-25 18:56:06,895] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:56:06,916] [INFO] ===== Completeness check finished =====
[2024-01-25 18:56:06,916] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:56:06,918] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900460155.1_52700_E01_genomic.fna/markers.fasta)
[2024-01-25 18:56:06,918] [INFO] Task started: Blastn
[2024-01-25 18:56:06,918] [INFO] Running command: blastn -query GCF_900460155.1_52700_E01_genomic.fna/markers.fasta -db /var/lib/cwl/stg23223516-bf0b-438e-a657-0ce2bcac2a8d/dqc_reference/reference_markers_gtdb.fasta -out GCF_900460155.1_52700_E01_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:56:08,901] [INFO] Task succeeded: Blastn
[2024-01-25 18:56:08,904] [INFO] Selected 8 target genomes.
[2024-01-25 18:56:08,904] [INFO] Target genome list was writen to GCF_900460155.1_52700_E01_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:56:08,916] [INFO] Task started: fastANI
[2024-01-25 18:56:08,917] [INFO] Running command: fastANI --query /var/lib/cwl/stg93fd7127-77a2-438e-ad4b-44b32546f24b/GCF_900460155.1_52700_E01_genomic.fna.gz --refList GCF_900460155.1_52700_E01_genomic.fna/target_genomes_gtdb.txt --output GCF_900460155.1_52700_E01_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:56:19,447] [INFO] Task succeeded: fastANI
[2024-01-25 18:56:19,453] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:56:19,454] [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_900103175.1	s__Tsukamurella pulmonis	99.9994	1583	1591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.49	98.89	0.96	0.93	5	conclusive
GCF_900104775.1	s__Tsukamurella tyrosinosolvens	88.8669	1314	1591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.14	98.76	0.95	0.91	8	-
GCF_007858475.1	s__Tsukamurella conjunctivitidis	88.3956	1272	1591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	99.89	99.89	0.98	0.98	2	-
GCF_007858445.1	s__Tsukamurella sputi	88.1969	1227	1591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900631615.1	s__Tsukamurella paurometabola_A	87.9126	1288	1591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007858435.1	s__Tsukamurella asaccharolytica	87.7286	1098	1591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001575205.1	s__Tsukamurella pseudospumae	86.2898	1218	1591	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Tsukamurella	95.0	98.07	98.07	0.92	0.92	2	-
GCF_012396015.1	s__Tsukamurella spumae	86.2268	1095	1591	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 18:56:19,455] [INFO] GTDB search result was written to GCF_900460155.1_52700_E01_genomic.fna/result_gtdb.tsv
[2024-01-25 18:56:19,456] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:56:19,458] [INFO] DFAST_QC result json was written to GCF_900460155.1_52700_E01_genomic.fna/dqc_result.json
[2024-01-25 18:56:19,458] [INFO] DFAST_QC completed!
[2024-01-25 18:56:19,458] [INFO] Total running time: 0h1m44s