[2024-01-24 15:02:36,390] [INFO] DFAST_QC pipeline started.
[2024-01-24 15:02:36,392] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 15:02:36,392] [INFO] DQC Reference Directory: /var/lib/cwl/stg78a61dab-bcbc-4a4b-9079-c26587e187a5/dqc_reference
[2024-01-24 15:02:38,279] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 15:02:38,281] [INFO] Task started: Prodigal
[2024-01-24 15:02:38,282] [INFO] Running command: gunzip -c /var/lib/cwl/stg9ed1970a-46a4-41a9-8ee7-400b9c76303d/GCF_019890715.1_ASM1989071v1_genomic.fna.gz | prodigal -d GCF_019890715.1_ASM1989071v1_genomic.fna/cds.fna -a GCF_019890715.1_ASM1989071v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 15:03:17,371] [INFO] Task succeeded: Prodigal
[2024-01-24 15:03:17,371] [INFO] Task started: HMMsearch
[2024-01-24 15:03:17,371] [INFO] Running command: hmmsearch --tblout GCF_019890715.1_ASM1989071v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg78a61dab-bcbc-4a4b-9079-c26587e187a5/dqc_reference/reference_markers.hmm GCF_019890715.1_ASM1989071v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 15:03:17,916] [INFO] Task succeeded: HMMsearch
[2024-01-24 15:03:17,918] [INFO] Found 6/6 markers.
[2024-01-24 15:03:17,999] [INFO] Query marker FASTA was written to GCF_019890715.1_ASM1989071v1_genomic.fna/markers.fasta
[2024-01-24 15:03:17,999] [INFO] Task started: Blastn
[2024-01-24 15:03:17,999] [INFO] Running command: blastn -query GCF_019890715.1_ASM1989071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78a61dab-bcbc-4a4b-9079-c26587e187a5/dqc_reference/reference_markers.fasta -out GCF_019890715.1_ASM1989071v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:03:19,267] [INFO] Task succeeded: Blastn
[2024-01-24 15:03:19,271] [INFO] Selected 10 target genomes.
[2024-01-24 15:03:19,271] [INFO] Target genome list was writen to GCF_019890715.1_ASM1989071v1_genomic.fna/target_genomes.txt
[2024-01-24 15:03:19,283] [INFO] Task started: fastANI
[2024-01-24 15:03:19,283] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ed1970a-46a4-41a9-8ee7-400b9c76303d/GCF_019890715.1_ASM1989071v1_genomic.fna.gz --refList GCF_019890715.1_ASM1989071v1_genomic.fna/target_genomes.txt --output GCF_019890715.1_ASM1989071v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 15:03:43,855] [INFO] Task succeeded: fastANI
[2024-01-24 15:03:43,856] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg78a61dab-bcbc-4a4b-9079-c26587e187a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 15:03:43,856] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg78a61dab-bcbc-4a4b-9079-c26587e187a5/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 15:03:43,865] [INFO] Found 10 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 15:03:43,865] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 15:03:43,865] [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
Nocardia coffeae	strain=CA2R105	GCA_019890715.1	2873381	2873381	type	True	100.0	3486	3486	95	inconclusive
Nocardia jiangxiensis	strain=NBRC 101359	GCA_000308615.1	282685	282685	type	True	95.4889	2679	3486	95	inconclusive
Nocardia miyunensis	strain=NBRC 108239	GCA_001613065.1	282684	282684	type	True	89.6341	2326	3486	95	below_threshold
Nocardia vaccinii	strain=NBRC 15922	GCA_001613305.1	1822	1822	type	True	89.1066	2193	3486	95	below_threshold
Nocardia macrotermitis	strain=RB20	GCA_009604405.1	2585198	2585198	type	True	88.0232	2243	3486	95	below_threshold
Nocardia albiluteola	strain=NEAU-G5	GCA_018860155.1	2842303	2842303	type	True	82.9369	1655	3486	95	below_threshold
Nocardia kruczakiae	strain=NBRC 101016	GCA_001612965.1	261477	261477	type	True	80.8947	1313	3486	95	below_threshold
Nocardia otitidiscaviarum	strain=NCTC1934	GCA_900454305.1	1823	1823	type	True	80.006	1096	3486	95	below_threshold
Nocardia otitidiscaviarum	strain=NBRC 14405	GCA_000308635.1	1823	1823	type	True	79.9705	1082	3486	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	79.5447	1145	3486	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 15:03:43,867] [INFO] DFAST Taxonomy check result was written to GCF_019890715.1_ASM1989071v1_genomic.fna/tc_result.tsv
[2024-01-24 15:03:43,867] [INFO] ===== Taxonomy check completed =====
[2024-01-24 15:03:43,868] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 15:03:43,868] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg78a61dab-bcbc-4a4b-9079-c26587e187a5/dqc_reference/checkm_data
[2024-01-24 15:03:43,869] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 15:03:43,961] [INFO] Task started: CheckM
[2024-01-24 15:03:43,961] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_019890715.1_ASM1989071v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_019890715.1_ASM1989071v1_genomic.fna/checkm_input GCF_019890715.1_ASM1989071v1_genomic.fna/checkm_result
[2024-01-24 15:05:44,277] [INFO] Task succeeded: CheckM
[2024-01-24 15:05:44,278] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 15:05:44,315] [INFO] ===== Completeness check finished =====
[2024-01-24 15:05:44,315] [INFO] ===== Start GTDB Search =====
[2024-01-24 15:05:44,316] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_019890715.1_ASM1989071v1_genomic.fna/markers.fasta)
[2024-01-24 15:05:44,316] [INFO] Task started: Blastn
[2024-01-24 15:05:44,316] [INFO] Running command: blastn -query GCF_019890715.1_ASM1989071v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg78a61dab-bcbc-4a4b-9079-c26587e187a5/dqc_reference/reference_markers_gtdb.fasta -out GCF_019890715.1_ASM1989071v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 15:05:46,059] [INFO] Task succeeded: Blastn
[2024-01-24 15:05:46,062] [INFO] Selected 13 target genomes.
[2024-01-24 15:05:46,062] [INFO] Target genome list was writen to GCF_019890715.1_ASM1989071v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 15:05:46,071] [INFO] Task started: fastANI
[2024-01-24 15:05:46,071] [INFO] Running command: fastANI --query /var/lib/cwl/stg9ed1970a-46a4-41a9-8ee7-400b9c76303d/GCF_019890715.1_ASM1989071v1_genomic.fna.gz --refList GCF_019890715.1_ASM1989071v1_genomic.fna/target_genomes_gtdb.txt --output GCF_019890715.1_ASM1989071v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 15:06:13,023] [INFO] Task succeeded: fastANI
[2024-01-24 15:06:13,039] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 15:06:13,039] [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_000308615.1	s__Nocardia jiangxiensis	95.4831	2680	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001613065.1	s__Nocardia miyunensis	89.6372	2327	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613305.1	s__Nocardia vaccinii	89.1016	2194	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009604405.1	s__Nocardia sp009604405	88.022	2243	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018860155.1	s__Nocardia sp018860155	82.924	1659	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612965.1	s__Nocardia kruczakiae	80.9067	1310	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.6988	N/A	N/A	N/A	N/A	1	-
GCF_001613105.1	s__Nocardia pseudobrasiliensis	80.8538	1292	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	0.99	0.99	2	-
GCF_002933465.1	s__Nocardia nova_B	80.7766	1205	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.92	99.92	0.99	0.99	2	-
GCF_000523235.1	s__Nocardia nova_A	80.7547	1374	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308635.1	s__Nocardia otitidiscaviarum	79.9647	1082	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.88	97.41	0.94	0.92	8	-
GCF_006716565.1	s__Nocardia bhagyanarayanae	79.5941	1135	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613045.1	s__Nocardia lijiangensis	79.5736	1090	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613425.1	s__Nocardia vulneris	79.4906	1125	3486	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	-
--------------------------------------------------------------------------------
[2024-01-24 15:06:13,041] [INFO] GTDB search result was written to GCF_019890715.1_ASM1989071v1_genomic.fna/result_gtdb.tsv
[2024-01-24 15:06:13,041] [INFO] ===== GTDB Search completed =====
[2024-01-24 15:06:13,047] [INFO] DFAST_QC result json was written to GCF_019890715.1_ASM1989071v1_genomic.fna/dqc_result.json
[2024-01-24 15:06:13,047] [INFO] DFAST_QC completed!
[2024-01-24 15:06:13,047] [INFO] Total running time: 0h3m37s