[2024-01-25 19:43:05,496] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:43:05,497] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:43:05,497] [INFO] DQC Reference Directory: /var/lib/cwl/stgb3ef6c0f-b971-41f7-b884-352f5f77eea9/dqc_reference
[2024-01-25 19:43:06,632] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:43:06,632] [INFO] Task started: Prodigal
[2024-01-25 19:43:06,633] [INFO] Running command: gunzip -c /var/lib/cwl/stg2adc347e-127c-4abf-9cdb-1cf3f213a47c/GCF_001613085.1_ASM161308v1_genomic.fna.gz | prodigal -d GCF_001613085.1_ASM161308v1_genomic.fna/cds.fna -a GCF_001613085.1_ASM161308v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:43:41,888] [INFO] Task succeeded: Prodigal
[2024-01-25 19:43:41,888] [INFO] Task started: HMMsearch
[2024-01-25 19:43:41,888] [INFO] Running command: hmmsearch --tblout GCF_001613085.1_ASM161308v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgb3ef6c0f-b971-41f7-b884-352f5f77eea9/dqc_reference/reference_markers.hmm GCF_001613085.1_ASM161308v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:43:42,204] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:43:42,205] [INFO] Found 6/6 markers.
[2024-01-25 19:43:42,270] [INFO] Query marker FASTA was written to GCF_001613085.1_ASM161308v1_genomic.fna/markers.fasta
[2024-01-25 19:43:42,270] [INFO] Task started: Blastn
[2024-01-25 19:43:42,270] [INFO] Running command: blastn -query GCF_001613085.1_ASM161308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3ef6c0f-b971-41f7-b884-352f5f77eea9/dqc_reference/reference_markers.fasta -out GCF_001613085.1_ASM161308v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:43:43,469] [INFO] Task succeeded: Blastn
[2024-01-25 19:43:43,471] [INFO] Selected 11 target genomes.
[2024-01-25 19:43:43,472] [INFO] Target genome list was writen to GCF_001613085.1_ASM161308v1_genomic.fna/target_genomes.txt
[2024-01-25 19:43:43,487] [INFO] Task started: fastANI
[2024-01-25 19:43:43,488] [INFO] Running command: fastANI --query /var/lib/cwl/stg2adc347e-127c-4abf-9cdb-1cf3f213a47c/GCF_001613085.1_ASM161308v1_genomic.fna.gz --refList GCF_001613085.1_ASM161308v1_genomic.fna/target_genomes.txt --output GCF_001613085.1_ASM161308v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:44:03,640] [INFO] Task succeeded: fastANI
[2024-01-25 19:44:03,641] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgb3ef6c0f-b971-41f7-b884-352f5f77eea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:44:03,641] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgb3ef6c0f-b971-41f7-b884-352f5f77eea9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:44:03,649] [INFO] Found 11 fastANI hits (2 hits with ANI > threshold)
[2024-01-25 19:44:03,649] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 19:44:03,649] [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 salmonicida	strain=NBRC 13393	GCA_001613085.1	53431	53431	type	True	100.0	2699	2704	95	conclusive
Nocardia salmonicida subsp. cummidelens	strain=NBRC 100378	GCA_001612865.1	2800120	53431	type	True	97.4063	2202	2704	95	conclusive
Nocardia fluminea	strain=DSM 44489	GCA_002846365.1	134984	134984	type	True	90.9552	2094	2704	95	below_threshold
Nocardia alba	strain=DSM 44684	GCA_004339125.1	225051	225051	type	True	89.8971	1883	2704	95	below_threshold
Nocardia alba	strain=NBRC 108234	GCA_001612665.1	225051	225051	type	True	89.8762	1892	2704	95	below_threshold
Nocardia rhizosphaerihabitans	strain=CGMCC 4.7329	GCA_014646295.1	1691570	1691570	type	True	85.9837	1732	2704	95	below_threshold
Nocardia rosealba	strain=NEAU-G4	GCA_020216065.1	2878563	2878563	type	True	84.5657	1565	2704	95	below_threshold
Nocardia shimofusensis	strain=NBRC 100134	GCA_001613125.1	228596	228596	type	True	80.5687	1030	2704	95	below_threshold
Nocardia higoensis	strain=NBRC 100133	GCA_000308595.1	228599	228599	type	True	80.463	1018	2704	95	below_threshold
Nocardia iowensis	strain=NRRL 5646	GCA_019222765.1	204891	204891	type	True	80.2413	1143	2704	95	below_threshold
Nocardia noduli	strain=ncl1	GCA_019038455.1	2815722	2815722	type	True	80.2091	1110	2704	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:44:03,650] [INFO] DFAST Taxonomy check result was written to GCF_001613085.1_ASM161308v1_genomic.fna/tc_result.tsv
[2024-01-25 19:44:03,651] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:44:03,651] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:44:03,651] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgb3ef6c0f-b971-41f7-b884-352f5f77eea9/dqc_reference/checkm_data
[2024-01-25 19:44:03,652] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:44:03,730] [INFO] Task started: CheckM
[2024-01-25 19:44:03,731] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613085.1_ASM161308v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613085.1_ASM161308v1_genomic.fna/checkm_input GCF_001613085.1_ASM161308v1_genomic.fna/checkm_result
[2024-01-25 19:45:40,907] [INFO] Task succeeded: CheckM
[2024-01-25 19:45:40,909] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.78%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:45:40,928] [INFO] ===== Completeness check finished =====
[2024-01-25 19:45:40,929] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:45:40,930] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613085.1_ASM161308v1_genomic.fna/markers.fasta)
[2024-01-25 19:45:40,930] [INFO] Task started: Blastn
[2024-01-25 19:45:40,930] [INFO] Running command: blastn -query GCF_001613085.1_ASM161308v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgb3ef6c0f-b971-41f7-b884-352f5f77eea9/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613085.1_ASM161308v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:45:42,788] [INFO] Task succeeded: Blastn
[2024-01-25 19:45:42,790] [INFO] Selected 12 target genomes.
[2024-01-25 19:45:42,791] [INFO] Target genome list was writen to GCF_001613085.1_ASM161308v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:45:42,797] [INFO] Task started: fastANI
[2024-01-25 19:45:42,798] [INFO] Running command: fastANI --query /var/lib/cwl/stg2adc347e-127c-4abf-9cdb-1cf3f213a47c/GCF_001613085.1_ASM161308v1_genomic.fna.gz --refList GCF_001613085.1_ASM161308v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613085.1_ASM161308v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:46:05,189] [INFO] Task succeeded: fastANI
[2024-01-25 19:46:05,198] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:46:05,198] [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_001613085.1	s__Nocardia salmonicida	100.0	2699	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.01	95.63	0.88	0.85	5	conclusive
GCF_002846365.1	s__Nocardia fluminea	90.9716	2092	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612665.1	s__Nocardia alba	89.895	1890	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
GCA_014360565.1	s__Nocardia sp014360565	89.282	1566	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_014646295.1	s__Nocardia rhizosphaerihabitans	85.9623	1735	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001886715.1	s__Nocardia mangyaensis	85.8316	1679	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612905.1	s__Nocardia ignorata	84.7727	1594	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_001612805.1	s__Nocardia coubleae	84.7468	1559	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.9719	100.00	100.00	1.00	1.00	2	-
GCF_013839555.1	s__Nocardia sp013839555	84.323	1220	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.2705	N/A	N/A	N/A	N/A	1	-
GCF_001613125.1	s__Nocardia shimofusensis	80.6025	1026	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308595.1	s__Nocardia higoensis	80.4603	1019	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_019222765.1	s__Nocardia iowensis	80.2448	1142	2704	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 19:46:05,200] [INFO] GTDB search result was written to GCF_001613085.1_ASM161308v1_genomic.fna/result_gtdb.tsv
[2024-01-25 19:46:05,200] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:46:05,205] [INFO] DFAST_QC result json was written to GCF_001613085.1_ASM161308v1_genomic.fna/dqc_result.json
[2024-01-25 19:46:05,205] [INFO] DFAST_QC completed!
[2024-01-25 19:46:05,205] [INFO] Total running time: 0h2m60s