[2024-01-24 12:54:05,369] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:54:05,373] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:54:05,374] [INFO] DQC Reference Directory: /var/lib/cwl/stgdf25e4ad-2529-455c-bc0a-6891f0a424f4/dqc_reference
[2024-01-24 12:54:07,722] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:54:07,723] [INFO] Task started: Prodigal
[2024-01-24 12:54:07,724] [INFO] Running command: gunzip -c /var/lib/cwl/stg98636553-158f-43a6-9cdf-af3a130f424e/GCF_009760405.1_ASM976040v1_genomic.fna.gz | prodigal -d GCF_009760405.1_ASM976040v1_genomic.fna/cds.fna -a GCF_009760405.1_ASM976040v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:54:40,668] [INFO] Task succeeded: Prodigal
[2024-01-24 12:54:40,669] [INFO] Task started: HMMsearch
[2024-01-24 12:54:40,669] [INFO] Running command: hmmsearch --tblout GCF_009760405.1_ASM976040v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgdf25e4ad-2529-455c-bc0a-6891f0a424f4/dqc_reference/reference_markers.hmm GCF_009760405.1_ASM976040v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:54:41,155] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:54:41,156] [INFO] Found 6/6 markers.
[2024-01-24 12:54:41,230] [INFO] Query marker FASTA was written to GCF_009760405.1_ASM976040v1_genomic.fna/markers.fasta
[2024-01-24 12:54:41,231] [INFO] Task started: Blastn
[2024-01-24 12:54:41,231] [INFO] Running command: blastn -query GCF_009760405.1_ASM976040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf25e4ad-2529-455c-bc0a-6891f0a424f4/dqc_reference/reference_markers.fasta -out GCF_009760405.1_ASM976040v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:54:42,524] [INFO] Task succeeded: Blastn
[2024-01-24 12:54:42,527] [INFO] Selected 10 target genomes.
[2024-01-24 12:54:42,528] [INFO] Target genome list was writen to GCF_009760405.1_ASM976040v1_genomic.fna/target_genomes.txt
[2024-01-24 12:54:42,537] [INFO] Task started: fastANI
[2024-01-24 12:54:42,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg98636553-158f-43a6-9cdf-af3a130f424e/GCF_009760405.1_ASM976040v1_genomic.fna.gz --refList GCF_009760405.1_ASM976040v1_genomic.fna/target_genomes.txt --output GCF_009760405.1_ASM976040v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:55:05,584] [INFO] Task succeeded: fastANI
[2024-01-24 12:55:05,584] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgdf25e4ad-2529-455c-bc0a-6891f0a424f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:55:05,584] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgdf25e4ad-2529-455c-bc0a-6891f0a424f4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:55:05,594] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:55:05,594] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:55:05,594] [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 terrae	strain=ET3-3	GCA_009760405.1	2675851	2675851	type	True	100.0	3093	3096	95	conclusive
Nocardia seriolae	strain=NBRC 15557	GCA_007990715.1	37332	37332	type	True	88.3344	1988	3096	95	below_threshold
Nocardia concava	strain=NBRC 100430	GCA_000308815.1	257281	257281	type	True	88.1786	2210	3096	95	below_threshold
Nocardia yunnanensis	strain=CFH S0054	GCA_003626895.1	2382165	2382165	type	True	87.026	2023	3096	95	below_threshold
Nocardia niigatensis	strain=NBRC 100131	GCA_000308655.1	209249	209249	type	True	86.8316	1971	3096	95	below_threshold
Nocardia tengchongensis	strain=CFH S0057	GCA_018362975.1	2055889	2055889	type	True	86.3728	1925	3096	95	below_threshold
Nocardia huaxiensis	strain=WCH-YHL-001	GCA_013744875.1	2755382	2755382	type	True	83.0869	1694	3096	95	below_threshold
Nocardia jejuensis	strain=NBRC 103114	GCA_001613145.1	328049	328049	type	True	82.6194	1619	3096	95	below_threshold
Nocardia uniformis	strain=JCM 3224	GCA_013004475.1	53432	53432	type	True	80.8558	1419	3096	95	below_threshold
Nocardia uniformis	strain=NBRC 13702	GCA_001613345.1	53432	53432	type	True	80.7452	1395	3096	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:55:05,596] [INFO] DFAST Taxonomy check result was written to GCF_009760405.1_ASM976040v1_genomic.fna/tc_result.tsv
[2024-01-24 12:55:05,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:55:05,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:55:05,597] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgdf25e4ad-2529-455c-bc0a-6891f0a424f4/dqc_reference/checkm_data
[2024-01-24 12:55:05,598] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:55:05,682] [INFO] Task started: CheckM
[2024-01-24 12:55:05,682] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_009760405.1_ASM976040v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_009760405.1_ASM976040v1_genomic.fna/checkm_input GCF_009760405.1_ASM976040v1_genomic.fna/checkm_result
[2024-01-24 12:56:49,307] [INFO] Task succeeded: CheckM
[2024-01-24 12:56:49,308] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 6.94%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:56:49,341] [INFO] ===== Completeness check finished =====
[2024-01-24 12:56:49,341] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:56:49,342] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_009760405.1_ASM976040v1_genomic.fna/markers.fasta)
[2024-01-24 12:56:49,342] [INFO] Task started: Blastn
[2024-01-24 12:56:49,342] [INFO] Running command: blastn -query GCF_009760405.1_ASM976040v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgdf25e4ad-2529-455c-bc0a-6891f0a424f4/dqc_reference/reference_markers_gtdb.fasta -out GCF_009760405.1_ASM976040v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:56:51,182] [INFO] Task succeeded: Blastn
[2024-01-24 12:56:51,186] [INFO] Selected 11 target genomes.
[2024-01-24 12:56:51,186] [INFO] Target genome list was writen to GCF_009760405.1_ASM976040v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:56:51,211] [INFO] Task started: fastANI
[2024-01-24 12:56:51,212] [INFO] Running command: fastANI --query /var/lib/cwl/stg98636553-158f-43a6-9cdf-af3a130f424e/GCF_009760405.1_ASM976040v1_genomic.fna.gz --refList GCF_009760405.1_ASM976040v1_genomic.fna/target_genomes_gtdb.txt --output GCF_009760405.1_ASM976040v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:57:15,356] [INFO] Task succeeded: fastANI
[2024-01-24 12:57:15,375] [INFO] Found 11 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:57:15,376] [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_009760405.1	s__Nocardia terrae	100.0	3093	3096	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_007990715.1	s__Nocardia seriolae	88.3405	1987	3096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	99.94	99.87	0.97	0.93	20	-
GCF_000308815.1	s__Nocardia concava	88.1625	2213	3096	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	87.0034	2027	3096	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	86.8399	1969	3096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009708175.1	s__Nocardia sp009708175	86.5774	1851	3096	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	86.3902	1923	3096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013744875.1	s__Nocardia sp013744875	83.1132	1687	3096	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	82.9212	1683	3096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613145.1	s__Nocardia jejuensis	82.6121	1620	3096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001613345.1	s__Nocardia uniformis	80.7479	1395	3096	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Nocardia	95.0	100.00	100.00	1.00	1.00	2	-
--------------------------------------------------------------------------------
[2024-01-24 12:57:15,378] [INFO] GTDB search result was written to GCF_009760405.1_ASM976040v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:57:15,379] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:57:15,387] [INFO] DFAST_QC result json was written to GCF_009760405.1_ASM976040v1_genomic.fna/dqc_result.json
[2024-01-24 12:57:15,388] [INFO] DFAST_QC completed!
[2024-01-24 12:57:15,388] [INFO] Total running time: 0h3m10s