[2024-01-25 17:37:20,902] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:37:20,904] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:37:20,904] [INFO] DQC Reference Directory: /var/lib/cwl/stg319f6f26-8982-4a0e-82ac-4e5dd1c94fb9/dqc_reference
[2024-01-25 17:37:22,040] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:37:22,040] [INFO] Task started: Prodigal
[2024-01-25 17:37:22,041] [INFO] Running command: gunzip -c /var/lib/cwl/stgd7ec6d2c-9802-410d-8bb5-6764fb8f1302/GCF_023501985.1_ASM2350198v1_genomic.fna.gz | prodigal -d GCF_023501985.1_ASM2350198v1_genomic.fna/cds.fna -a GCF_023501985.1_ASM2350198v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:38:03,059] [INFO] Task succeeded: Prodigal
[2024-01-25 17:38:03,060] [INFO] Task started: HMMsearch
[2024-01-25 17:38:03,060] [INFO] Running command: hmmsearch --tblout GCF_023501985.1_ASM2350198v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg319f6f26-8982-4a0e-82ac-4e5dd1c94fb9/dqc_reference/reference_markers.hmm GCF_023501985.1_ASM2350198v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:38:03,400] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:38:03,404] [INFO] Found 6/6 markers.
[2024-01-25 17:38:03,468] [INFO] Query marker FASTA was written to GCF_023501985.1_ASM2350198v1_genomic.fna/markers.fasta
[2024-01-25 17:38:03,468] [INFO] Task started: Blastn
[2024-01-25 17:38:03,468] [INFO] Running command: blastn -query GCF_023501985.1_ASM2350198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg319f6f26-8982-4a0e-82ac-4e5dd1c94fb9/dqc_reference/reference_markers.fasta -out GCF_023501985.1_ASM2350198v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:38:04,650] [INFO] Task succeeded: Blastn
[2024-01-25 17:38:04,654] [INFO] Selected 14 target genomes.
[2024-01-25 17:38:04,654] [INFO] Target genome list was writen to GCF_023501985.1_ASM2350198v1_genomic.fna/target_genomes.txt
[2024-01-25 17:38:04,658] [INFO] Task started: fastANI
[2024-01-25 17:38:04,659] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ec6d2c-9802-410d-8bb5-6764fb8f1302/GCF_023501985.1_ASM2350198v1_genomic.fna.gz --refList GCF_023501985.1_ASM2350198v1_genomic.fna/target_genomes.txt --output GCF_023501985.1_ASM2350198v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:38:31,395] [INFO] Task succeeded: fastANI
[2024-01-25 17:38:31,395] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg319f6f26-8982-4a0e-82ac-4e5dd1c94fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:38:31,396] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg319f6f26-8982-4a0e-82ac-4e5dd1c94fb9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:38:31,405] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 17:38:31,405] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 17:38:31,405] [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 gipuzkoensis	strain=234509	GCA_013839485.1	2749991	2749991	type	True	89.507	1975	2646	95	below_threshold
Nocardia abscessus	strain=NBRC 100374	GCA_000308455.1	120957	120957	suspected-type	True	89.4727	1958	2646	95	below_threshold
Nocardia abscessus	strain=FDAARGOS_1596	GCA_020731305.1	120957	120957	suspected-type	True	89.4708	2007	2646	95	below_threshold
Nocardia barduliensis	strain=335427	GCA_013315795.1	2736643	2736643	type	True	89.0091	1881	2646	95	below_threshold
Nocardia exalbida	strain=NBRC 100660	GCA_000308575.1	290231	290231	type	True	88.9415	1845	2646	95	below_threshold
Nocardia gamkensis	strain=NRRL B-24450	GCA_013181665.1	352869	352869	type	True	88.929	1918	2646	95	below_threshold
Nocardia gamkensis	strain=NBRC 108242	GCA_001612985.1	352869	352869	type	True	88.9222	1898	2646	95	below_threshold
Nocardia gamkensis	strain=DSM 44956	GCA_012396055.1	352869	352869	type	True	88.9019	1920	2646	95	below_threshold
Nocardia arthritidis	strain=NBRC 100137	GCA_001612765.1	228602	228602	type	True	88.8253	1872	2646	95	below_threshold
Nocardia asiatica	strain=NBRC 100129	GCA_000308415.1	209252	209252	type	True	88.6378	1835	2646	95	below_threshold
Nocardia niwae	strain=NBRC 108934	GCA_001613465.1	626084	626084	type	True	88.4351	1872	2646	95	below_threshold
Nocardia araoensis	strain=NBRC 100135	GCA_000308435.1	228600	228600	type	True	88.3544	1777	2646	95	below_threshold
Nocardia beijingensis	strain=NBRC 16342	GCA_001612785.1	95162	95162	type	True	88.1717	1815	2646	95	below_threshold
Nocardia pneumoniae	strain=NBRC 100136	GCA_000308755.1	228601	228601	type	True	86.7801	1763	2646	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:38:31,406] [INFO] DFAST Taxonomy check result was written to GCF_023501985.1_ASM2350198v1_genomic.fna/tc_result.tsv
[2024-01-25 17:38:31,407] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:38:31,407] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:38:31,407] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg319f6f26-8982-4a0e-82ac-4e5dd1c94fb9/dqc_reference/checkm_data
[2024-01-25 17:38:31,408] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:38:31,486] [INFO] Task started: CheckM
[2024-01-25 17:38:31,486] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_023501985.1_ASM2350198v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_023501985.1_ASM2350198v1_genomic.fna/checkm_input GCF_023501985.1_ASM2350198v1_genomic.fna/checkm_result
[2024-01-25 17:40:20,323] [INFO] Task succeeded: CheckM
[2024-01-25 17:40:20,324] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 27.78%
Strain heterogeneity: 75.00%
--------------------------------------------------------------------------------
[2024-01-25 17:40:20,374] [INFO] ===== Completeness check finished =====
[2024-01-25 17:40:20,374] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:40:20,376] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_023501985.1_ASM2350198v1_genomic.fna/markers.fasta)
[2024-01-25 17:40:20,376] [INFO] Task started: Blastn
[2024-01-25 17:40:20,376] [INFO] Running command: blastn -query GCF_023501985.1_ASM2350198v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg319f6f26-8982-4a0e-82ac-4e5dd1c94fb9/dqc_reference/reference_markers_gtdb.fasta -out GCF_023501985.1_ASM2350198v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:40:22,242] [INFO] Task succeeded: Blastn
[2024-01-25 17:40:22,244] [INFO] Selected 14 target genomes.
[2024-01-25 17:40:22,245] [INFO] Target genome list was writen to GCF_023501985.1_ASM2350198v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:40:22,259] [INFO] Task started: fastANI
[2024-01-25 17:40:22,260] [INFO] Running command: fastANI --query /var/lib/cwl/stgd7ec6d2c-9802-410d-8bb5-6764fb8f1302/GCF_023501985.1_ASM2350198v1_genomic.fna.gz --refList GCF_023501985.1_ASM2350198v1_genomic.fna/target_genomes_gtdb.txt --output GCF_023501985.1_ASM2350198v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:40:53,389] [INFO] Task succeeded: fastANI
[2024-01-25 17:40:53,398] [INFO] Found 14 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:40:53,399] [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_009829295.1	s__Nocardia sp009829295	99.4012	2295	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.64	99.39	0.96	0.94	4	conclusive
GCF_000308455.1	s__Nocardia abscessus	89.4656	1959	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.07	95.78	0.84	0.83	5	-
GCF_015477775.1	s__Nocardia abscessus_A	89.3009	2003	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013315795.1	s__Nocardia barduliensis	89.0142	1881	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308575.1	s__Nocardia exalbida	88.9463	1844	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	N/A	N/A	N/A	N/A	1	-
GCF_001612985.1	s__Nocardia gamkensis	88.9222	1898	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	96.7192	100.00	100.00	1.00	0.99	3	-
GCF_001612765.1	s__Nocardia arthritidis	88.8286	1871	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.103	N/A	N/A	N/A	N/A	1	-
GCF_000308415.1	s__Nocardia asiatica	88.6534	1833	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613465.1	s__Nocardia niwae	88.4451	1871	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000308435.1	s__Nocardia araoensis	88.371	1775	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009829325.1	s__Nocardia sp009829325	88.2923	1917	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	96.48	96.48	0.88	0.88	2	-
GCF_001612785.1	s__Nocardia beijingensis	88.1866	1813	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	98.03	98.03	0.92	0.92	2	-
GCF_000308755.1	s__Nocardia pneumoniae	86.7806	1763	2646	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_015477605.1	s__Nocardia amamiensis_A	86.3046	1761	2646	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 17:40:53,400] [INFO] GTDB search result was written to GCF_023501985.1_ASM2350198v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:40:53,401] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:40:53,404] [INFO] DFAST_QC result json was written to GCF_023501985.1_ASM2350198v1_genomic.fna/dqc_result.json
[2024-01-25 17:40:53,405] [INFO] DFAST_QC completed!
[2024-01-25 17:40:53,405] [INFO] Total running time: 0h3m33s