[2024-01-24 11:58:56,801] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:58:56,803] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:58:56,803] [INFO] DQC Reference Directory: /var/lib/cwl/stg24d8c833-e282-4f31-8ed5-a126d1321cd2/dqc_reference
[2024-01-24 11:58:58,172] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:58:58,173] [INFO] Task started: Prodigal
[2024-01-24 11:58:58,173] [INFO] Running command: gunzip -c /var/lib/cwl/stg9b3abb46-dd40-45cc-9ab0-798e9a41524b/GCF_003183825.1_ASM318382v1_genomic.fna.gz | prodigal -d GCF_003183825.1_ASM318382v1_genomic.fna/cds.fna -a GCF_003183825.1_ASM318382v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:59:31,648] [INFO] Task succeeded: Prodigal
[2024-01-24 11:59:31,648] [INFO] Task started: HMMsearch
[2024-01-24 11:59:31,648] [INFO] Running command: hmmsearch --tblout GCF_003183825.1_ASM318382v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg24d8c833-e282-4f31-8ed5-a126d1321cd2/dqc_reference/reference_markers.hmm GCF_003183825.1_ASM318382v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:59:31,989] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:59:31,990] [INFO] Found 6/6 markers.
[2024-01-24 11:59:32,039] [INFO] Query marker FASTA was written to GCF_003183825.1_ASM318382v1_genomic.fna/markers.fasta
[2024-01-24 11:59:32,040] [INFO] Task started: Blastn
[2024-01-24 11:59:32,040] [INFO] Running command: blastn -query GCF_003183825.1_ASM318382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d8c833-e282-4f31-8ed5-a126d1321cd2/dqc_reference/reference_markers.fasta -out GCF_003183825.1_ASM318382v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:59:33,206] [INFO] Task succeeded: Blastn
[2024-01-24 11:59:33,210] [INFO] Selected 5 target genomes.
[2024-01-24 11:59:33,210] [INFO] Target genome list was writen to GCF_003183825.1_ASM318382v1_genomic.fna/target_genomes.txt
[2024-01-24 11:59:33,225] [INFO] Task started: fastANI
[2024-01-24 11:59:33,225] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b3abb46-dd40-45cc-9ab0-798e9a41524b/GCF_003183825.1_ASM318382v1_genomic.fna.gz --refList GCF_003183825.1_ASM318382v1_genomic.fna/target_genomes.txt --output GCF_003183825.1_ASM318382v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:59:42,166] [INFO] Task succeeded: fastANI
[2024-01-24 11:59:42,166] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg24d8c833-e282-4f31-8ed5-a126d1321cd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:59:42,167] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg24d8c833-e282-4f31-8ed5-a126d1321cd2/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:59:42,173] [INFO] Found 5 fastANI hits (5 hits with ANI > threshold)
[2024-01-24 11:59:42,173] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:59:42,173] [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
Gordonia terrae	strain=NRRL B-16283	GCA_003183825.1	2055	2055	suspected-type	True	100.0	1902	1902	95	conclusive
Gordonia terrae	strain=3612	GCA_001698225.1	2055	2055	suspected-type	True	99.9943	1899	1902	95	conclusive
Gordonia terrae	strain=NCTC10669	GCA_901542405.1	2055	2055	suspected-type	True	99.9942	1898	1902	95	conclusive
Gordonia terrae	strain=NRRL B-16283	GCA_000716975.1	2055	2055	suspected-type	True	99.9751	1852	1902	95	conclusive
Gordonia terrae	strain=NBRC 100016	GCA_000248035.2	2055	2055	suspected-type	True	99.936	1834	1902	95	conclusive
--------------------------------------------------------------------------------
[2024-01-24 11:59:42,175] [INFO] DFAST Taxonomy check result was written to GCF_003183825.1_ASM318382v1_genomic.fna/tc_result.tsv
[2024-01-24 11:59:42,175] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:59:42,175] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:59:42,176] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg24d8c833-e282-4f31-8ed5-a126d1321cd2/dqc_reference/checkm_data
[2024-01-24 11:59:42,176] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:59:42,228] [INFO] Task started: CheckM
[2024-01-24 11:59:42,229] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003183825.1_ASM318382v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003183825.1_ASM318382v1_genomic.fna/checkm_input GCF_003183825.1_ASM318382v1_genomic.fna/checkm_result
[2024-01-24 12:01:42,039] [INFO] Task succeeded: CheckM
[2024-01-24 12:01:42,040] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:01:42,058] [INFO] ===== Completeness check finished =====
[2024-01-24 12:01:42,058] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:01:42,059] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003183825.1_ASM318382v1_genomic.fna/markers.fasta)
[2024-01-24 12:01:42,059] [INFO] Task started: Blastn
[2024-01-24 12:01:42,059] [INFO] Running command: blastn -query GCF_003183825.1_ASM318382v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg24d8c833-e282-4f31-8ed5-a126d1321cd2/dqc_reference/reference_markers_gtdb.fasta -out GCF_003183825.1_ASM318382v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:01:43,715] [INFO] Task succeeded: Blastn
[2024-01-24 12:01:43,718] [INFO] Selected 7 target genomes.
[2024-01-24 12:01:43,718] [INFO] Target genome list was writen to GCF_003183825.1_ASM318382v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:01:43,723] [INFO] Task started: fastANI
[2024-01-24 12:01:43,723] [INFO] Running command: fastANI --query /var/lib/cwl/stg9b3abb46-dd40-45cc-9ab0-798e9a41524b/GCF_003183825.1_ASM318382v1_genomic.fna.gz --refList GCF_003183825.1_ASM318382v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003183825.1_ASM318382v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:01:54,175] [INFO] Task succeeded: fastANI
[2024-01-24 12:01:54,182] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:01:54,182] [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_001698225.1	s__Gordonia terrae	99.9943	1899	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.37	97.67	0.96	0.87	7	conclusive
GCF_002149015.1	s__Gordonia lacunae	91.7667	1573	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000143885.2	s__Gordonia sp000143885	89.5344	1520	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.85	97.53	0.90	0.88	3	-
GCF_011290605.1	s__Gordonia sp002009645	88.9805	1507	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	97.70	97.37	0.91	0.88	14	-
GCA_014041935.1	s__Gordonia sp014041935	83.3295	1217	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	99.20	99.20	0.95	0.95	2	-
GCF_900105725.1	s__Gordonia westfalica	83.1236	1274	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000327325.1	s__Gordonia rubripertincta	83.0847	1146	1902	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Mycobacteriales;f__Mycobacteriaceae;g__Gordonia	95.0	98.55	98.07	0.91	0.87	6	-
--------------------------------------------------------------------------------
[2024-01-24 12:01:54,184] [INFO] GTDB search result was written to GCF_003183825.1_ASM318382v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:01:54,184] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:01:54,187] [INFO] DFAST_QC result json was written to GCF_003183825.1_ASM318382v1_genomic.fna/dqc_result.json
[2024-01-24 12:01:54,187] [INFO] DFAST_QC completed!
[2024-01-24 12:01:54,187] [INFO] Total running time: 0h2m57s