[2024-01-24 12:06:24,601] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:06:24,603] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:06:24,603] [INFO] DQC Reference Directory: /var/lib/cwl/stg1ca0a210-6626-4de9-9c7f-2364dd41ca94/dqc_reference
[2024-01-24 12:06:25,857] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:06:25,858] [INFO] Task started: Prodigal
[2024-01-24 12:06:25,859] [INFO] Running command: gunzip -c /var/lib/cwl/stg11357d24-e5be-4047-9321-076ce2644faa/GCF_900197875.1_FRACA_ARgP5_genomic.fna.gz | prodigal -d GCF_900197875.1_FRACA_ARgP5_genomic.fna/cds.fna -a GCF_900197875.1_FRACA_ARgP5_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:06:44,827] [INFO] Task succeeded: Prodigal
[2024-01-24 12:06:44,828] [INFO] Task started: HMMsearch
[2024-01-24 12:06:44,828] [INFO] Running command: hmmsearch --tblout GCF_900197875.1_FRACA_ARgP5_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1ca0a210-6626-4de9-9c7f-2364dd41ca94/dqc_reference/reference_markers.hmm GCF_900197875.1_FRACA_ARgP5_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:06:45,129] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:06:45,130] [INFO] Found 6/6 markers.
[2024-01-24 12:06:45,199] [INFO] Query marker FASTA was written to GCF_900197875.1_FRACA_ARgP5_genomic.fna/markers.fasta
[2024-01-24 12:06:45,200] [INFO] Task started: Blastn
[2024-01-24 12:06:45,200] [INFO] Running command: blastn -query GCF_900197875.1_FRACA_ARgP5_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca0a210-6626-4de9-9c7f-2364dd41ca94/dqc_reference/reference_markers.fasta -out GCF_900197875.1_FRACA_ARgP5_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:06:46,415] [INFO] Task succeeded: Blastn
[2024-01-24 12:06:46,418] [INFO] Selected 14 target genomes.
[2024-01-24 12:06:46,418] [INFO] Target genome list was writen to GCF_900197875.1_FRACA_ARgP5_genomic.fna/target_genomes.txt
[2024-01-24 12:06:46,428] [INFO] Task started: fastANI
[2024-01-24 12:06:46,428] [INFO] Running command: fastANI --query /var/lib/cwl/stg11357d24-e5be-4047-9321-076ce2644faa/GCF_900197875.1_FRACA_ARgP5_genomic.fna.gz --refList GCF_900197875.1_FRACA_ARgP5_genomic.fna/target_genomes.txt --output GCF_900197875.1_FRACA_ARgP5_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:07:06,909] [INFO] Task succeeded: fastANI
[2024-01-24 12:07:06,909] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1ca0a210-6626-4de9-9c7f-2364dd41ca94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:07:06,909] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1ca0a210-6626-4de9-9c7f-2364dd41ca94/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:07:06,920] [INFO] Found 14 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 12:07:06,920] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 12:07:06,920] [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
Frankia canadensis		GCA_900197875.1	1836972	1836972	type	True	100.0	2246	2270	95	conclusive
Frankia alni	strain=ACN14a	GCA_000058485.1	1859	1859	type	True	83.0434	1319	2270	95	below_threshold
Frankia torreyi	strain=CpI1	GCA_000948395.1	1856	1856	type	True	82.956	1320	2270	95	below_threshold
Candidatus Frankia alpina		GCA_902806485.1	2699483	2699483	type	True	82.897	1027	2270	95	below_threshold
Frankia casuarinae	strain=CcI3	GCA_000013345.1	106370	106370	type	True	80.9618	888	2270	95	below_threshold
Frankia elaeagni	strain=BMG5.12	GCA_000374165.1	222534	222534	type	True	79.2637	925	2270	95	below_threshold
Frankia irregularis	strain=DSM 45899	GCA_001536285.1	795642	795642	type	True	79.0469	987	2270	95	below_threshold
Pseudonocardia bannensis	strain=DSM 45300	GCA_012911875.1	630973	630973	type	True	76.1764	467	2270	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_017164735.1	1436133	1436133	type	True	76.035	528	2270	95	below_threshold
Nocardioides solisilvae	strain=Ka25	GCA_003194625.1	1542435	1542435	type	True	75.9977	383	2270	95	below_threshold
Actinacidiphila paucisporea	strain=CGMCC 4.2025	GCA_900142575.1	310782	310782	type	True	75.9938	596	2270	95	below_threshold
Actinacidiphila bryophytorum	strain=DSM 42138	GCA_016916835.1	1436133	1436133	type	True	75.993	581	2270	95	below_threshold
Pseudokineococcus marinus	strain=JCM 14547	GCA_013004605.1	351215	351215	type	True	75.8389	327	2270	95	below_threshold
Microbacterium immunditiarum	strain=DSM 24662	GCA_013409785.1	337480	337480	type	True	75.4574	224	2270	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:07:06,922] [INFO] DFAST Taxonomy check result was written to GCF_900197875.1_FRACA_ARgP5_genomic.fna/tc_result.tsv
[2024-01-24 12:07:06,922] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:07:06,923] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:07:06,923] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1ca0a210-6626-4de9-9c7f-2364dd41ca94/dqc_reference/checkm_data
[2024-01-24 12:07:06,924] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:07:06,996] [INFO] Task started: CheckM
[2024-01-24 12:07:06,996] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_900197875.1_FRACA_ARgP5_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_900197875.1_FRACA_ARgP5_genomic.fna/checkm_input GCF_900197875.1_FRACA_ARgP5_genomic.fna/checkm_result
[2024-01-24 12:08:05,928] [INFO] Task succeeded: CheckM
[2024-01-24 12:08:05,929] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:08:05,951] [INFO] ===== Completeness check finished =====
[2024-01-24 12:08:05,951] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:08:05,952] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_900197875.1_FRACA_ARgP5_genomic.fna/markers.fasta)
[2024-01-24 12:08:05,952] [INFO] Task started: Blastn
[2024-01-24 12:08:05,952] [INFO] Running command: blastn -query GCF_900197875.1_FRACA_ARgP5_genomic.fna/markers.fasta -db /var/lib/cwl/stg1ca0a210-6626-4de9-9c7f-2364dd41ca94/dqc_reference/reference_markers_gtdb.fasta -out GCF_900197875.1_FRACA_ARgP5_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:08:07,605] [INFO] Task succeeded: Blastn
[2024-01-24 12:08:07,609] [INFO] Selected 13 target genomes.
[2024-01-24 12:08:07,609] [INFO] Target genome list was writen to GCF_900197875.1_FRACA_ARgP5_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:08:07,644] [INFO] Task started: fastANI
[2024-01-24 12:08:07,644] [INFO] Running command: fastANI --query /var/lib/cwl/stg11357d24-e5be-4047-9321-076ce2644faa/GCF_900197875.1_FRACA_ARgP5_genomic.fna.gz --refList GCF_900197875.1_FRACA_ARgP5_genomic.fna/target_genomes_gtdb.txt --output GCF_900197875.1_FRACA_ARgP5_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:08:25,504] [INFO] Task succeeded: fastANI
[2024-01-24 12:08:25,515] [INFO] Found 13 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:08:25,515] [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_900197875.1	s__Frankia canadensis	100.0	2246	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	100.00	100.00	0.99	0.99	2	conclusive
GCF_000262465.1	s__Frankia sp000262465	83.091	1306	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000058485.1	s__Frankia alni	83.0261	1322	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.50	99.50	0.95	0.95	2	-
GCF_000948395.1	s__Frankia torreyi	82.9625	1319	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.67	99.51	0.95	0.92	3	-
GCF_902806485.1	s__Frankia sp902806485	82.9085	1024	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_902806475.1	s__Frankia nodulisporulans	82.2411	912	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.88	99.87	0.86	0.85	3	-
GCF_000013345.1	s__Frankia casuarinae	80.9564	889	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.59	99.21	0.94	0.87	12	-
GCF_001854655.1	s__Frankia sp001854655	79.2768	930	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000177675.1	s__Frankia sp000177675	79.0457	963	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_016916835.1	s__Streptomyces bryophytorum	76.0115	575	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptomycetales;f__Streptomycetaceae;g__Streptomyces	95.0	99.96	99.96	0.99	0.99	2	-
GCF_001750215.1	s__Xylanimonas variabilis_A	75.936	349	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Xylanimonas	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013004605.1	s__Pseudokineococcus marinus	75.8559	320	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Quadrisphaeraceae;g__Pseudokineococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013204985.1	s__Rathayibacter sp013204985	75.669	206	2270	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rathayibacter	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 12:08:25,517] [INFO] GTDB search result was written to GCF_900197875.1_FRACA_ARgP5_genomic.fna/result_gtdb.tsv
[2024-01-24 12:08:25,518] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:08:25,522] [INFO] DFAST_QC result json was written to GCF_900197875.1_FRACA_ARgP5_genomic.fna/dqc_result.json
[2024-01-24 12:08:25,522] [INFO] DFAST_QC completed!
[2024-01-24 12:08:25,522] [INFO] Total running time: 0h2m1s