[2024-01-25 18:39:50,649] [INFO] DFAST_QC pipeline started.
[2024-01-25 18:39:50,650] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 18:39:50,650] [INFO] DQC Reference Directory: /var/lib/cwl/stgaf32a667-4833-4a4f-898f-b8d8321dd603/dqc_reference
[2024-01-25 18:39:51,767] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 18:39:51,767] [INFO] Task started: Prodigal
[2024-01-25 18:39:51,768] [INFO] Running command: gunzip -c /var/lib/cwl/stgd26e4007-b876-4bf0-9275-3105efee9ece/GCF_000373365.1_ASM37336v1_genomic.fna.gz | prodigal -d GCF_000373365.1_ASM37336v1_genomic.fna/cds.fna -a GCF_000373365.1_ASM37336v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 18:40:10,736] [INFO] Task succeeded: Prodigal
[2024-01-25 18:40:10,736] [INFO] Task started: HMMsearch
[2024-01-25 18:40:10,737] [INFO] Running command: hmmsearch --tblout GCF_000373365.1_ASM37336v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgaf32a667-4833-4a4f-898f-b8d8321dd603/dqc_reference/reference_markers.hmm GCF_000373365.1_ASM37336v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 18:40:11,015] [INFO] Task succeeded: HMMsearch
[2024-01-25 18:40:11,016] [INFO] Found 6/6 markers.
[2024-01-25 18:40:11,073] [INFO] Query marker FASTA was written to GCF_000373365.1_ASM37336v1_genomic.fna/markers.fasta
[2024-01-25 18:40:11,074] [INFO] Task started: Blastn
[2024-01-25 18:40:11,074] [INFO] Running command: blastn -query GCF_000373365.1_ASM37336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf32a667-4833-4a4f-898f-b8d8321dd603/dqc_reference/reference_markers.fasta -out GCF_000373365.1_ASM37336v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:40:12,154] [INFO] Task succeeded: Blastn
[2024-01-25 18:40:12,157] [INFO] Selected 12 target genomes.
[2024-01-25 18:40:12,157] [INFO] Target genome list was writen to GCF_000373365.1_ASM37336v1_genomic.fna/target_genomes.txt
[2024-01-25 18:40:12,161] [INFO] Task started: fastANI
[2024-01-25 18:40:12,161] [INFO] Running command: fastANI --query /var/lib/cwl/stgd26e4007-b876-4bf0-9275-3105efee9ece/GCF_000373365.1_ASM37336v1_genomic.fna.gz --refList GCF_000373365.1_ASM37336v1_genomic.fna/target_genomes.txt --output GCF_000373365.1_ASM37336v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 18:40:35,115] [INFO] Task succeeded: fastANI
[2024-01-25 18:40:35,116] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgaf32a667-4833-4a4f-898f-b8d8321dd603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 18:40:35,116] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgaf32a667-4833-4a4f-898f-b8d8321dd603/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 18:40:35,124] [INFO] Found 12 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 18:40:35,124] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 18:40:35,124] [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 discariae	strain=BCU110501	GCA_000373365.1	365528	365528	type	True	100.0	2524	2537	95	conclusive
Frankia soli	strain=NRRL B-16219	GCA_001854695.1	2599596	2599596	type	True	91.9689	1889	2537	95	below_threshold
Frankia elaeagni	strain=BMG5.12	GCA_000374165.1	222534	222534	type	True	83.0304	1516	2537	95	below_threshold
Frankia irregularis	strain=DSM 45899	GCA_001536285.1	795642	795642	type	True	82.2334	1540	2537	95	below_threshold
Frankia canadensis		GCA_900197875.1	1836972	1836972	type	True	79.5199	1015	2537	95	below_threshold
Frankia torreyi	strain=CpI1	GCA_000948395.1	1856	1856	type	True	79.4482	1079	2537	95	below_threshold
Frankia casuarinae	strain=CcI3	GCA_000013345.1	106370	106370	type	True	79.3405	792	2537	95	below_threshold
Candidatus Frankia alpina		GCA_902806485.1	2699483	2699483	type	True	79.3365	811	2537	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	78.6893	1096	2537	95	below_threshold
Frankia inefficax	strain=EuI1c	GCA_000166135.1	298654	298654	type	True	78.5428	1094	2537	95	below_threshold
Actinomadura macrotermitis	strain=RB68	GCA_009604375.1	2585200	2585200	type	True	75.9989	808	2537	95	below_threshold
Pseudokineococcus lusitanus	strain=CECT 7306	GCA_003751265.1	763993	763993	type	True	75.5344	509	2537	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 18:40:35,125] [INFO] DFAST Taxonomy check result was written to GCF_000373365.1_ASM37336v1_genomic.fna/tc_result.tsv
[2024-01-25 18:40:35,129] [INFO] ===== Taxonomy check completed =====
[2024-01-25 18:40:35,129] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 18:40:35,129] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgaf32a667-4833-4a4f-898f-b8d8321dd603/dqc_reference/checkm_data
[2024-01-25 18:40:35,130] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 18:40:35,205] [INFO] Task started: CheckM
[2024-01-25 18:40:35,205] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000373365.1_ASM37336v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000373365.1_ASM37336v1_genomic.fna/checkm_input GCF_000373365.1_ASM37336v1_genomic.fna/checkm_result
[2024-01-25 18:41:38,557] [INFO] Task succeeded: CheckM
[2024-01-25 18:41:38,558] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 18:41:38,580] [INFO] ===== Completeness check finished =====
[2024-01-25 18:41:38,581] [INFO] ===== Start GTDB Search =====
[2024-01-25 18:41:38,581] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000373365.1_ASM37336v1_genomic.fna/markers.fasta)
[2024-01-25 18:41:38,581] [INFO] Task started: Blastn
[2024-01-25 18:41:38,581] [INFO] Running command: blastn -query GCF_000373365.1_ASM37336v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgaf32a667-4833-4a4f-898f-b8d8321dd603/dqc_reference/reference_markers_gtdb.fasta -out GCF_000373365.1_ASM37336v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 18:41:40,257] [INFO] Task succeeded: Blastn
[2024-01-25 18:41:40,264] [INFO] Selected 12 target genomes.
[2024-01-25 18:41:40,264] [INFO] Target genome list was writen to GCF_000373365.1_ASM37336v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 18:41:40,270] [INFO] Task started: fastANI
[2024-01-25 18:41:40,270] [INFO] Running command: fastANI --query /var/lib/cwl/stgd26e4007-b876-4bf0-9275-3105efee9ece/GCF_000373365.1_ASM37336v1_genomic.fna.gz --refList GCF_000373365.1_ASM37336v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000373365.1_ASM37336v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 18:42:03,251] [INFO] Task succeeded: fastANI
[2024-01-25 18:42:03,260] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 18:42:03,260] [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_000373365.1	s__Frankia discariae	100.0	2524	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001854695.1	s__Frankia soli	91.9808	1888	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	97.36	96.57	0.84	0.84	3	-
GCF_000374165.1	s__Frankia elaeagni	83.0257	1516	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854655.1	s__Frankia sp001854655	82.9823	1580	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001636565.1	s__Frankia sp001636565	82.9414	1353	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001536285.1	s__Frankia irregularis	82.2764	1530	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	97.56	96.33	0.90	0.84	4	-
GCF_000177675.1	s__Frankia sp000177675	82.267	1475	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000262465.1	s__Frankia sp000262465	79.3032	1102	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001983105.1	s__Frankia asymbiotica	78.6717	1100	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001552555.1	s__Nocardiopsis_B trehalosi	75.8002	636	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Streptosporangiales;f__Streptosporangiaceae;g__Nocardiopsis_B	95.0	N/A	N/A	N/A	N/A	1	-
GCF_007991755.1	s__Cellulomonas aerilata	75.6167	415	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
GCA_014763765.1	s__Cellulomonas sp014763765	75.4996	436	2537	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Cellulomonadaceae;g__Cellulomonas	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 18:42:03,262] [INFO] GTDB search result was written to GCF_000373365.1_ASM37336v1_genomic.fna/result_gtdb.tsv
[2024-01-25 18:42:03,263] [INFO] ===== GTDB Search completed =====
[2024-01-25 18:42:03,266] [INFO] DFAST_QC result json was written to GCF_000373365.1_ASM37336v1_genomic.fna/dqc_result.json
[2024-01-25 18:42:03,267] [INFO] DFAST_QC completed!
[2024-01-25 18:42:03,267] [INFO] Total running time: 0h2m13s