[2024-01-24 14:31:14,828] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:31:14,830] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:31:14,830] [INFO] DQC Reference Directory: /var/lib/cwl/stg6a7fc2a6-9aca-4fa3-bf7a-4774186676fe/dqc_reference
[2024-01-24 14:31:16,258] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:31:16,259] [INFO] Task started: Prodigal
[2024-01-24 14:31:16,259] [INFO] Running command: gunzip -c /var/lib/cwl/stgbe7caf02-b863-4723-b9af-016df5a2ed71/GCF_001613405.1_ASM161340v1_genomic.fna.gz | prodigal -d GCF_001613405.1_ASM161340v1_genomic.fna/cds.fna -a GCF_001613405.1_ASM161340v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:31:49,405] [INFO] Task succeeded: Prodigal
[2024-01-24 14:31:49,405] [INFO] Task started: HMMsearch
[2024-01-24 14:31:49,406] [INFO] Running command: hmmsearch --tblout GCF_001613405.1_ASM161340v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg6a7fc2a6-9aca-4fa3-bf7a-4774186676fe/dqc_reference/reference_markers.hmm GCF_001613405.1_ASM161340v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:31:49,761] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:31:49,762] [INFO] Found 6/6 markers.
[2024-01-24 14:31:49,833] [INFO] Query marker FASTA was written to GCF_001613405.1_ASM161340v1_genomic.fna/markers.fasta
[2024-01-24 14:31:49,833] [INFO] Task started: Blastn
[2024-01-24 14:31:49,833] [INFO] Running command: blastn -query GCF_001613405.1_ASM161340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a7fc2a6-9aca-4fa3-bf7a-4774186676fe/dqc_reference/reference_markers.fasta -out GCF_001613405.1_ASM161340v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:31:51,051] [INFO] Task succeeded: Blastn
[2024-01-24 14:31:51,057] [INFO] Selected 13 target genomes.
[2024-01-24 14:31:51,057] [INFO] Target genome list was writen to GCF_001613405.1_ASM161340v1_genomic.fna/target_genomes.txt
[2024-01-24 14:31:51,062] [INFO] Task started: fastANI
[2024-01-24 14:31:51,062] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7caf02-b863-4723-b9af-016df5a2ed71/GCF_001613405.1_ASM161340v1_genomic.fna.gz --refList GCF_001613405.1_ASM161340v1_genomic.fna/target_genomes.txt --output GCF_001613405.1_ASM161340v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:32:17,218] [INFO] Task succeeded: fastANI
[2024-01-24 14:32:17,219] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg6a7fc2a6-9aca-4fa3-bf7a-4774186676fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:32:17,219] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg6a7fc2a6-9aca-4fa3-bf7a-4774186676fe/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:32:17,234] [INFO] Found 13 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 14:32:17,234] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 14:32:17,235] [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 crassostreae	strain=NBRC 100342	GCA_001613405.1	53428	53428	type	True	100.0	2732	2738	95	conclusive
Nocardia huaxiensis	strain=WCH-YHL-001	GCA_013744875.1	2755382	2755382	type	True	83.3296	1666	2738	95	below_threshold
Nocardia seriolae	strain=NBRC 15557	GCA_007990715.1	37332	37332	type	True	83.2598	1491	2738	95	below_threshold
Nocardia yamanashiensis	strain=NBRC 100130	GCA_001613325.1	209247	209247	type	True	83.2072	1644	2738	95	below_threshold
Nocardia concava	strain=NBRC 100430	GCA_000308815.1	257281	257281	type	True	83.1131	1594	2738	95	below_threshold
Nocardia acididurans	strain=LPG 2	GCA_016741815.1	2802282	2802282	type	True	83.0115	1666	2738	95	below_threshold
Nocardia yunnanensis	strain=CFH S0054	GCA_003626895.1	2382165	2382165	type	True	82.9739	1504	2738	95	below_threshold
Nocardia inohanensis	strain=NBRC 100128	GCA_001612945.1	209246	209246	type	True	82.9245	1634	2738	95	below_threshold
Nocardia tengchongensis	strain=CFH S0057	GCA_018362975.1	2055889	2055889	type	True	82.9072	1472	2738	95	below_threshold
Nocardia terrae	strain=ET3-3	GCA_009760405.1	2675851	2675851	type	True	82.8917	1605	2738	95	below_threshold
Nocardia niigatensis	strain=NBRC 100131	GCA_000308655.1	209249	209249	type	True	82.7993	1497	2738	95	below_threshold
Nocardia otitidiscaviarum	strain=NBRC 14405	GCA_000308635.1	1823	1823	type	True	82.361	1458	2738	95	below_threshold
Nocardia otitidiscaviarum	strain=NCTC1934	GCA_900454305.1	1823	1823	type	True	82.3377	1508	2738	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:32:17,449] [INFO] DFAST Taxonomy check result was written to GCF_001613405.1_ASM161340v1_genomic.fna/tc_result.tsv
[2024-01-24 14:32:17,450] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:32:17,451] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:32:17,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg6a7fc2a6-9aca-4fa3-bf7a-4774186676fe/dqc_reference/checkm_data
[2024-01-24 14:32:17,453] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:32:17,528] [INFO] Task started: CheckM
[2024-01-24 14:32:17,528] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001613405.1_ASM161340v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001613405.1_ASM161340v1_genomic.fna/checkm_input GCF_001613405.1_ASM161340v1_genomic.fna/checkm_result
[2024-01-24 14:33:48,895] [INFO] Task succeeded: CheckM
[2024-01-24 14:33:48,896] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 2.31%
Strain heterogeneity: 40.00%
--------------------------------------------------------------------------------
[2024-01-24 14:33:48,924] [INFO] ===== Completeness check finished =====
[2024-01-24 14:33:48,925] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:33:48,925] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001613405.1_ASM161340v1_genomic.fna/markers.fasta)
[2024-01-24 14:33:48,926] [INFO] Task started: Blastn
[2024-01-24 14:33:48,926] [INFO] Running command: blastn -query GCF_001613405.1_ASM161340v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg6a7fc2a6-9aca-4fa3-bf7a-4774186676fe/dqc_reference/reference_markers_gtdb.fasta -out GCF_001613405.1_ASM161340v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:33:50,644] [INFO] Task succeeded: Blastn
[2024-01-24 14:33:50,648] [INFO] Selected 12 target genomes.
[2024-01-24 14:33:50,649] [INFO] Target genome list was writen to GCF_001613405.1_ASM161340v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:33:50,674] [INFO] Task started: fastANI
[2024-01-24 14:33:50,674] [INFO] Running command: fastANI --query /var/lib/cwl/stgbe7caf02-b863-4723-b9af-016df5a2ed71/GCF_001613405.1_ASM161340v1_genomic.fna.gz --refList GCF_001613405.1_ASM161340v1_genomic.fna/target_genomes_gtdb.txt --output GCF_001613405.1_ASM161340v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:34:15,022] [INFO] Task succeeded: fastANI
[2024-01-24 14:34:15,036] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:34:15,036] [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_001613405.1	s__Nocardia crassostreae	100.0	2732	2738	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_013744875.1	s__Nocardia sp013744875	83.3163	1668	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007990715.1	s__Nocardia seriolae	83.2994	1483	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.94	99.87	0.97	0.93	20	-
GCF_001613325.1	s__Nocardia yamanashiensis	83.1859	1647	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308815.1	s__Nocardia concava	83.1129	1594	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016741815.1	s__Nocardia sp016741815	83.0483	1660	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003626895.1	s__Nocardia yunnanensis	82.9627	1505	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_018362975.1	s__Nocardia tengchongensis	82.9363	1467	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001612945.1	s__Nocardia inohanensis	82.8977	1640	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009760405.1	s__Nocardia terrae	82.8794	1610	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308655.1	s__Nocardia niigatensis	82.8024	1497	2738	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	82.3718	1456	2738	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	97.88	97.41	0.94	0.92	8	-
--------------------------------------------------------------------------------
[2024-01-24 14:34:15,042] [INFO] GTDB search result was written to GCF_001613405.1_ASM161340v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:34:15,043] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:34:15,047] [INFO] DFAST_QC result json was written to GCF_001613405.1_ASM161340v1_genomic.fna/dqc_result.json
[2024-01-24 14:34:15,047] [INFO] DFAST_QC completed!
[2024-01-24 14:34:15,047] [INFO] Total running time: 0h3m0s