[2023-06-30 20:35:01,192] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:35:01,194] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:35:01,195] [INFO] DQC Reference Directory: /var/lib/cwl/stg287318c9-d2ec-479b-96a9-e5d5b21789ec/dqc_reference
[2023-06-30 20:35:02,416] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:35:02,416] [INFO] Task started: Prodigal
[2023-06-30 20:35:02,417] [INFO] Running command: gunzip -c /var/lib/cwl/stgf2a549ac-9722-4f98-ac3e-3e003c140411/GCA_024641095.1_ASM2464109v1_genomic.fna.gz | prodigal -d GCA_024641095.1_ASM2464109v1_genomic.fna/cds.fna -a GCA_024641095.1_ASM2464109v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:35:05,764] [INFO] Task succeeded: Prodigal
[2023-06-30 20:35:05,764] [INFO] Task started: HMMsearch
[2023-06-30 20:35:05,764] [INFO] Running command: hmmsearch --tblout GCA_024641095.1_ASM2464109v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg287318c9-d2ec-479b-96a9-e5d5b21789ec/dqc_reference/reference_markers.hmm GCA_024641095.1_ASM2464109v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:35:05,930] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:35:05,931] [INFO] Found 6/6 markers.
[2023-06-30 20:35:05,947] [INFO] Query marker FASTA was written to GCA_024641095.1_ASM2464109v1_genomic.fna/markers.fasta
[2023-06-30 20:35:05,948] [INFO] Task started: Blastn
[2023-06-30 20:35:05,948] [INFO] Running command: blastn -query GCA_024641095.1_ASM2464109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg287318c9-d2ec-479b-96a9-e5d5b21789ec/dqc_reference/reference_markers.fasta -out GCA_024641095.1_ASM2464109v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:35:06,510] [INFO] Task succeeded: Blastn
[2023-06-30 20:35:06,513] [INFO] Selected 18 target genomes.
[2023-06-30 20:35:06,513] [INFO] Target genome list was writen to GCA_024641095.1_ASM2464109v1_genomic.fna/target_genomes.txt
[2023-06-30 20:35:06,515] [INFO] Task started: fastANI
[2023-06-30 20:35:06,515] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a549ac-9722-4f98-ac3e-3e003c140411/GCA_024641095.1_ASM2464109v1_genomic.fna.gz --refList GCA_024641095.1_ASM2464109v1_genomic.fna/target_genomes.txt --output GCA_024641095.1_ASM2464109v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:35:14,485] [INFO] Task succeeded: fastANI
[2023-06-30 20:35:14,486] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg287318c9-d2ec-479b-96a9-e5d5b21789ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:35:14,486] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg287318c9-d2ec-479b-96a9-e5d5b21789ec/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:35:14,492] [INFO] Found 3 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:35:14,492] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:35:14,492] [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
Rhodoluna lacicola	strain=MWH-Ta8	GCA_000699505.1	529884	529884	type	True	81.652	246	395	95	below_threshold
Rhodoluna limnophila	strain=27D-LEPI	GCA_005845365.1	232537	232537	type	True	79.4358	157	395	95	below_threshold
Candidatus Rhodoluna planktonica	strain=MWH-Dar1	GCA_001854225.1	535712	535712	type	True	78.0584	88	395	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:35:14,494] [INFO] DFAST Taxonomy check result was written to GCA_024641095.1_ASM2464109v1_genomic.fna/tc_result.tsv
[2023-06-30 20:35:14,495] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:35:14,495] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:35:14,495] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg287318c9-d2ec-479b-96a9-e5d5b21789ec/dqc_reference/checkm_data
[2023-06-30 20:35:14,496] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:35:14,511] [INFO] Task started: CheckM
[2023-06-30 20:35:14,511] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024641095.1_ASM2464109v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024641095.1_ASM2464109v1_genomic.fna/checkm_input GCA_024641095.1_ASM2464109v1_genomic.fna/checkm_result
[2023-06-30 20:35:31,464] [INFO] Task succeeded: CheckM
[2023-06-30 20:35:31,465] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 92.59%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:35:31,484] [INFO] ===== Completeness check finished =====
[2023-06-30 20:35:31,484] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:35:31,484] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024641095.1_ASM2464109v1_genomic.fna/markers.fasta)
[2023-06-30 20:35:31,485] [INFO] Task started: Blastn
[2023-06-30 20:35:31,485] [INFO] Running command: blastn -query GCA_024641095.1_ASM2464109v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg287318c9-d2ec-479b-96a9-e5d5b21789ec/dqc_reference/reference_markers_gtdb.fasta -out GCA_024641095.1_ASM2464109v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:35:32,262] [INFO] Task succeeded: Blastn
[2023-06-30 20:35:32,266] [INFO] Selected 19 target genomes.
[2023-06-30 20:35:32,266] [INFO] Target genome list was writen to GCA_024641095.1_ASM2464109v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:35:32,270] [INFO] Task started: fastANI
[2023-06-30 20:35:32,271] [INFO] Running command: fastANI --query /var/lib/cwl/stgf2a549ac-9722-4f98-ac3e-3e003c140411/GCA_024641095.1_ASM2464109v1_genomic.fna.gz --refList GCA_024641095.1_ASM2464109v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024641095.1_ASM2464109v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:35:38,398] [INFO] Task succeeded: fastANI
[2023-06-30 20:35:38,409] [INFO] Found 10 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 20:35:38,409] [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_000699505.1	s__Rhodoluna lacicola	81.652	246	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005845365.1	s__Rhodoluna limnophila	79.4358	157	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.04	97.94	0.96	0.95	3	-
GCA_009703465.1	s__Rhodoluna sp009703465	78.7597	80	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	98.63	98.63	0.78	0.78	2	-
GCA_009703445.1	s__Rhodoluna sp009703445	78.7454	100	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903866485.1	s__Rhodoluna sp903866485	78.1175	76	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001854225.1	s__Rhodoluna planktonica	78.0584	88	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_017984715.1	s__Rhodoluna sp017984715	77.8381	65	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903927775.1	s__Rhodoluna sp903927775	77.7131	54	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903893675.1	s__Rhodoluna sp903893675	77.2617	70	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
GCA_009698805.1	s__Rhodoluna sp009698805	76.8907	52	395	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Actinomycetales;f__Microbacteriaceae;g__Rhodoluna	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:35:38,411] [INFO] GTDB search result was written to GCA_024641095.1_ASM2464109v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:35:38,412] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:35:38,414] [INFO] DFAST_QC result json was written to GCA_024641095.1_ASM2464109v1_genomic.fna/dqc_result.json
[2023-06-30 20:35:38,414] [INFO] DFAST_QC completed!
[2023-06-30 20:35:38,415] [INFO] Total running time: 0h0m37s