[2024-01-24 13:40:45,939] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:40:45,942] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:40:45,943] [INFO] DQC Reference Directory: /var/lib/cwl/stgbade2b81-16aa-41b6-96e5-e9b5cf21d074/dqc_reference
[2024-01-24 13:40:47,261] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:40:47,262] [INFO] Task started: Prodigal
[2024-01-24 13:40:47,262] [INFO] Running command: gunzip -c /var/lib/cwl/stg7a16a3c5-e4a3-4dbe-81d8-d5443ca4c034/GCF_001613425.1_ASM161342v1_genomic.fna.gz | prodigal -d GCF_001613425.1_ASM161342v1_genomic.fna/cds.fna -a GCF_001613425.1_ASM161342v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:41:28,238] [INFO] Task succeeded: Prodigal
[2024-01-24 13:41:28,239] [INFO] Task started: HMMsearch
[2024-01-24 13:41:28,239] [INFO] Running command: hmmsearch --tblout GCF_001613425.1_ASM161342v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbade2b81-16aa-41b6-96e5-e9b5cf21d074/dqc_reference/reference_markers.hmm GCF_001613425.1_ASM161342v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:41:28,632] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:41:28,634] [INFO] Found 6/6 markers.
[2024-01-24 13:41:28,706] [INFO] Query marker FASTA was written to GCF_001613425.1_ASM161342v1_genomic.fna/markers.fasta
[2024-01-24 13:41:28,707] [INFO] Task started: Blastn
[2024-01-24 13:41:28,707] [INFO] Running command: blastn -query GCF_001613425.1_ASM161342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbade2b81-16aa-41b6-96e5-e9b5cf21d074/dqc_reference/reference_markers.fasta -out GCF_001613425.1_ASM161342v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:41:29,973] [INFO] Task succeeded: Blastn
[2024-01-24 13:41:29,978] [INFO] Selected 12 target genomes.
[2024-01-24 13:41:29,978] [INFO] Target genome list was writen to GCF_001613425.1_ASM161342v1_genomic.fna/target_genomes.txt
[2024-01-24 13:41:30,078] [INFO] Task started: fastANI
[2024-01-24 13:41:30,078] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a16a3c5-e4a3-4dbe-81d8-d5443ca4c034/GCF_001613425.1_ASM161342v1_genomic.fna.gz --refList GCF_001613425.1_ASM161342v1_genomic.fna/target_genomes.txt --output GCF_001613425.1_ASM161342v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:41:57,971] [INFO] Task succeeded: fastANI
[2024-01-24 13:41:57,972] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbade2b81-16aa-41b6-96e5-e9b5cf21d074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:41:57,973] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbade2b81-16aa-41b6-96e5-e9b5cf21d074/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:41:57,986] [INFO] Found 12 fastANI hits (4 hits with ANI > threshold)
[2024-01-24 13:41:57,987] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:41:57,987] [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 vulneris	strain=NBRC 108936	GCA_001613425.1	1141657	1141657	type	True	100.0	3091	3092	95	inconclusive
Nocardia vulneris	strain=W9851	GCA_000811985.1	1141657	1141657	type	True	99.9755	3016	3092	95	inconclusive
Nocardia brasiliensis	strain=NCTC11294	GCA_900454265.1	37326	37326	suspected-type	True	95.7982	2751	3092	95	inconclusive
Nocardia brasiliensis	strain=NBRC 14402	GCA_000308475.2	37326	37326	suspected-type	True	95.7627	2695	3092	95	inconclusive
Nocardia colli	strain=CICC 11023	GCA_008704205.1	2545717	2545717	type	True	85.1097	2142	3092	95	below_threshold
Nocardia ninae	strain=NBRC 108245	GCA_007990755.1	356145	356145	type	True	84.9279	2015	3092	95	below_threshold
Nocardia tenerifensis	strain=NBRC 101015	GCA_000308715.1	228006	228006	type	True	84.7288	1855	3092	95	below_threshold
Nocardia altamirensis	strain=NBRC 108246	GCA_001612685.1	472158	472158	type	True	84.396	1924	3092	95	below_threshold
Nocardia abscessus	strain=FDAARGOS_1596	GCA_020731305.1	120957	120957	suspected-type	True	82.499	1446	3092	95	below_threshold
Nocardia bhagyanarayanae	strain=DSM 103495	GCA_006716565.1	1215925	1215925	type	True	82.166	1423	3092	95	below_threshold
Nocardia lijiangensis	strain=NBRC 108240	GCA_001613045.1	299618	299618	type	True	82.095	1370	3092	95	below_threshold
Nocardia farcinica	strain=DSM 43257	GCA_900156775.1	37329	37329	type	True	81.5775	1189	3092	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:41:57,989] [INFO] DFAST Taxonomy check result was written to GCF_001613425.1_ASM161342v1_genomic.fna/tc_result.tsv
[2024-01-24 13:41:57,989] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:41:57,989] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:41:57,989] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbade2b81-16aa-41b6-96e5-e9b5cf21d074/dqc_reference/checkm_data
[2024-01-24 13:41:57,991] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:41:58,073] [INFO] Task started: CheckM
[2024-01-24 13:41:58,073] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613425.1_ASM161342v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613425.1_ASM161342v1_genomic.fna/checkm_input GCF_001613425.1_ASM161342v1_genomic.fna/checkm_result
[2024-01-24 13:43:48,425] [INFO] Task succeeded: CheckM
[2024-01-24 13:43:48,427] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 10.65%
Strain heterogeneity: 42.86%
--------------------------------------------------------------------------------
[2024-01-24 13:43:48,459] [INFO] ===== Completeness check finished =====
[2024-01-24 13:43:48,459] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:43:48,459] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613425.1_ASM161342v1_genomic.fna/markers.fasta)
[2024-01-24 13:43:48,460] [INFO] Task started: Blastn
[2024-01-24 13:43:48,460] [INFO] Running command: blastn -query GCF_001613425.1_ASM161342v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbade2b81-16aa-41b6-96e5-e9b5cf21d074/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613425.1_ASM161342v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:43:50,332] [INFO] Task succeeded: Blastn
[2024-01-24 13:43:50,337] [INFO] Selected 7 target genomes.
[2024-01-24 13:43:50,337] [INFO] Target genome list was writen to GCF_001613425.1_ASM161342v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:43:50,388] [INFO] Task started: fastANI
[2024-01-24 13:43:50,389] [INFO] Running command: fastANI --query /var/lib/cwl/stg7a16a3c5-e4a3-4dbe-81d8-d5443ca4c034/GCF_001613425.1_ASM161342v1_genomic.fna.gz --refList GCF_001613425.1_ASM161342v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613425.1_ASM161342v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:44:07,255] [INFO] Task succeeded: fastANI
[2024-01-24 13:44:07,267] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:44:07,268] [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_001613425.1	s__Nocardia vulneris	100.0	3091	3092	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	100.00	0.99	0.99	2	conclusive
GCF_000308475.2	s__Nocardia brasiliensis	95.7627	2695	3092	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.8238	100.00	99.99	1.00	1.00	3	-
GCF_000250675.2	s__Nocardia brasiliensis_B	95.2192	2798	3092	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2192	100.00	100.00	1.00	1.00	2	conclusive
GCF_000710915.1	s__Nocardia brasiliensis_A	94.7315	2600	3092	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2054	98.35	98.32	0.89	0.89	3	-
GCF_011801125.1	s__Nocardia brasiliensis_C	89.6836	2266	3092	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612685.1	s__Nocardia altamirensis	84.3975	1924	3092	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	82.1058	1370	3092	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:44:07,270] [INFO] GTDB search result was written to GCF_001613425.1_ASM161342v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:44:07,270] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:44:07,274] [INFO] DFAST_QC result json was written to GCF_001613425.1_ASM161342v1_genomic.fna/dqc_result.json
[2024-01-24 13:44:07,274] [INFO] DFAST_QC completed!
[2024-01-24 13:44:07,274] [INFO] Total running time: 0h3m21s