[2024-01-24 11:05:49,412] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:05:49,417] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:05:49,417] [INFO] DQC Reference Directory: /var/lib/cwl/stge5d4b1b0-9e0d-401c-9fe6-dbd3326122bc/dqc_reference
[2024-01-24 11:05:51,278] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:05:51,279] [INFO] Task started: Prodigal
[2024-01-24 11:05:51,280] [INFO] Running command: gunzip -c /var/lib/cwl/stgdb4564ee-e97e-42b1-9647-22262f4b4a5b/GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna.gz | prodigal -d GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/cds.fna -a GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:06:16,789] [INFO] Task succeeded: Prodigal
[2024-01-24 11:06:16,789] [INFO] Task started: HMMsearch
[2024-01-24 11:06:16,789] [INFO] Running command: hmmsearch --tblout GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stge5d4b1b0-9e0d-401c-9fe6-dbd3326122bc/dqc_reference/reference_markers.hmm GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:06:17,083] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:06:17,084] [INFO] Found 6/6 markers.
[2024-01-24 11:06:17,144] [INFO] Query marker FASTA was written to GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/markers.fasta
[2024-01-24 11:06:17,144] [INFO] Task started: Blastn
[2024-01-24 11:06:17,144] [INFO] Running command: blastn -query GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge5d4b1b0-9e0d-401c-9fe6-dbd3326122bc/dqc_reference/reference_markers.fasta -out GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:06:18,226] [INFO] Task succeeded: Blastn
[2024-01-24 11:06:18,229] [INFO] Selected 10 target genomes.
[2024-01-24 11:06:18,229] [INFO] Target genome list was writen to GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/target_genomes.txt
[2024-01-24 11:06:18,244] [INFO] Task started: fastANI
[2024-01-24 11:06:18,244] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb4564ee-e97e-42b1-9647-22262f4b4a5b/GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna.gz --refList GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/target_genomes.txt --output GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:06:36,456] [INFO] Task succeeded: fastANI
[2024-01-24 11:06:36,456] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stge5d4b1b0-9e0d-401c-9fe6-dbd3326122bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:06:36,457] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stge5d4b1b0-9e0d-401c-9fe6-dbd3326122bc/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:06:36,468] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:06:36,469] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:06:36,469] [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 irregularis	strain=DSM 45899	GCA_001536285.1	795642	795642	type	True	100.0	3126	3135	95	conclusive
Frankia elaeagni	strain=BMG5.12	GCA_000374165.1	222534	222534	type	True	83.0014	1622	3135	95	below_threshold
Frankia soli	strain=NRRL B-16219	GCA_001854695.1	2599596	2599596	type	True	82.2599	1498	3135	95	below_threshold
Frankia discariae	strain=BCU110501	GCA_000373365.1	365528	365528	type	True	82.0452	1575	3135	95	below_threshold
Frankia casuarinae	strain=CcI3	GCA_000013345.1	106370	106370	type	True	79.0143	751	3135	95	below_threshold
Candidatus Frankia alpina		GCA_902806485.1	2699483	2699483	type	True	78.94	771	3135	95	below_threshold
Frankia canadensis		GCA_900197875.1	1836972	1836972	type	True	78.9279	1033	3135	95	below_threshold
Frankia alni	strain=ACN14a	GCA_000058485.1	1859	1859	type	True	78.6603	1054	3135	95	below_threshold
Frankia torreyi	strain=CpI1	GCA_000948395.1	1856	1856	type	True	78.6323	1037	3135	95	below_threshold
Frankia asymbiotica	strain=NRRL B-16386	GCA_001983105.1	1834516	1834516	type	True	78.3351	1158	3135	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:06:36,470] [INFO] DFAST Taxonomy check result was written to GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/tc_result.tsv
[2024-01-24 11:06:36,471] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:06:36,471] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:06:36,471] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stge5d4b1b0-9e0d-401c-9fe6-dbd3326122bc/dqc_reference/checkm_data
[2024-01-24 11:06:36,472] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:06:36,554] [INFO] Task started: CheckM
[2024-01-24 11:06:36,555] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/checkm_input GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/checkm_result
[2024-01-24 11:08:02,090] [INFO] Task succeeded: CheckM
[2024-01-24 11:08:02,091] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 11:08:02,114] [INFO] ===== Completeness check finished =====
[2024-01-24 11:08:02,114] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:08:02,114] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/markers.fasta)
[2024-01-24 11:08:02,115] [INFO] Task started: Blastn
[2024-01-24 11:08:02,115] [INFO] Running command: blastn -query GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/markers.fasta -db /var/lib/cwl/stge5d4b1b0-9e0d-401c-9fe6-dbd3326122bc/dqc_reference/reference_markers_gtdb.fasta -out GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:08:03,749] [INFO] Task succeeded: Blastn
[2024-01-24 11:08:03,752] [INFO] Selected 9 target genomes.
[2024-01-24 11:08:03,752] [INFO] Target genome list was writen to GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:08:03,763] [INFO] Task started: fastANI
[2024-01-24 11:08:03,763] [INFO] Running command: fastANI --query /var/lib/cwl/stgdb4564ee-e97e-42b1-9647-22262f4b4a5b/GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna.gz --refList GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/target_genomes_gtdb.txt --output GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:08:22,340] [INFO] Task succeeded: fastANI
[2024-01-24 11:08:22,348] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:08:22,349] [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_001536285.1	s__Frankia irregularis	100.0	3125	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	97.56	96.33	0.90	0.84	4	conclusive
GCF_000177675.1	s__Frankia sp000177675	94.8143	2329	3135	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	83.7714	1556	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000374165.1	s__Frankia elaeagni	82.9909	1623	3135	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	82.9894	1693	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854695.1	s__Frankia soli	82.2416	1501	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	97.36	96.57	0.84	0.84	3	-
GCF_000373365.1	s__Frankia discariae	82.0184	1580	3135	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	78.6653	1070	3135	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	78.6456	1057	3135	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Frankiaceae;g__Frankia	95.0	99.50	99.50	0.95	0.95	2	-
--------------------------------------------------------------------------------
[2024-01-24 11:08:22,350] [INFO] GTDB search result was written to GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/result_gtdb.tsv
[2024-01-24 11:08:22,351] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:08:22,353] [INFO] DFAST_QC result json was written to GCF_001536285.1_IMG-taxon_2634166352_annotated_assembly_genomic.fna/dqc_result.json
[2024-01-24 11:08:22,354] [INFO] DFAST_QC completed!
[2024-01-24 11:08:22,354] [INFO] Total running time: 0h2m33s