[2023-06-30 20:55:21,824] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:55:21,831] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:55:21,831] [INFO] DQC Reference Directory: /var/lib/cwl/stgff1b235d-72d6-49d2-878e-2b8fa9ccd2d6/dqc_reference
[2023-06-30 20:55:24,601] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:55:24,602] [INFO] Task started: Prodigal
[2023-06-30 20:55:24,603] [INFO] Running command: gunzip -c /var/lib/cwl/stg5af0ab9c-6f57-4b28-9415-d86b53e7aa25/GCA_024226335.1_ASM2422633v1_genomic.fna.gz | prodigal -d GCA_024226335.1_ASM2422633v1_genomic.fna/cds.fna -a GCA_024226335.1_ASM2422633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:55:39,748] [INFO] Task succeeded: Prodigal
[2023-06-30 20:55:39,749] [INFO] Task started: HMMsearch
[2023-06-30 20:55:39,749] [INFO] Running command: hmmsearch --tblout GCA_024226335.1_ASM2422633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgff1b235d-72d6-49d2-878e-2b8fa9ccd2d6/dqc_reference/reference_markers.hmm GCA_024226335.1_ASM2422633v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:55:40,081] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:55:40,083] [INFO] Found 6/6 markers.
[2023-06-30 20:55:40,136] [INFO] Query marker FASTA was written to GCA_024226335.1_ASM2422633v1_genomic.fna/markers.fasta
[2023-06-30 20:55:40,136] [INFO] Task started: Blastn
[2023-06-30 20:55:40,137] [INFO] Running command: blastn -query GCA_024226335.1_ASM2422633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff1b235d-72d6-49d2-878e-2b8fa9ccd2d6/dqc_reference/reference_markers.fasta -out GCA_024226335.1_ASM2422633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:40,839] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:40,843] [INFO] Selected 27 target genomes.
[2023-06-30 20:55:40,844] [INFO] Target genome list was writen to GCA_024226335.1_ASM2422633v1_genomic.fna/target_genomes.txt
[2023-06-30 20:55:40,851] [INFO] Task started: fastANI
[2023-06-30 20:55:40,851] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af0ab9c-6f57-4b28-9415-d86b53e7aa25/GCA_024226335.1_ASM2422633v1_genomic.fna.gz --refList GCA_024226335.1_ASM2422633v1_genomic.fna/target_genomes.txt --output GCA_024226335.1_ASM2422633v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:56:01,143] [INFO] Task succeeded: fastANI
[2023-06-30 20:56:01,143] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgff1b235d-72d6-49d2-878e-2b8fa9ccd2d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:56:01,143] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgff1b235d-72d6-49d2-878e-2b8fa9ccd2d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:56:01,147] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:56:01,147] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-30 20:56:01,147] [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
Paraburkholderia heleia	strain=NBRC 101817	GCA_000739775.1	634127	634127	type	True	74.7267	54	1667	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-30 20:56:01,149] [INFO] DFAST Taxonomy check result was written to GCA_024226335.1_ASM2422633v1_genomic.fna/tc_result.tsv
[2023-06-30 20:56:01,150] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:56:01,150] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:56:01,150] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgff1b235d-72d6-49d2-878e-2b8fa9ccd2d6/dqc_reference/checkm_data
[2023-06-30 20:56:01,151] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:56:01,218] [INFO] Task started: CheckM
[2023-06-30 20:56:01,219] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_024226335.1_ASM2422633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_024226335.1_ASM2422633v1_genomic.fna/checkm_input GCA_024226335.1_ASM2422633v1_genomic.fna/checkm_result
[2023-06-30 20:56:46,699] [INFO] Task succeeded: CheckM
[2023-06-30 20:56:46,700] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 99.07%
Contamintation: 2.08%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:56:46,725] [INFO] ===== Completeness check finished =====
[2023-06-30 20:56:46,726] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:56:46,726] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_024226335.1_ASM2422633v1_genomic.fna/markers.fasta)
[2023-06-30 20:56:46,726] [INFO] Task started: Blastn
[2023-06-30 20:56:46,727] [INFO] Running command: blastn -query GCA_024226335.1_ASM2422633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgff1b235d-72d6-49d2-878e-2b8fa9ccd2d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_024226335.1_ASM2422633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:56:47,778] [INFO] Task succeeded: Blastn
[2023-06-30 20:56:47,782] [INFO] Selected 21 target genomes.
[2023-06-30 20:56:47,783] [INFO] Target genome list was writen to GCA_024226335.1_ASM2422633v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:56:47,810] [INFO] Task started: fastANI
[2023-06-30 20:56:47,810] [INFO] Running command: fastANI --query /var/lib/cwl/stg5af0ab9c-6f57-4b28-9415-d86b53e7aa25/GCA_024226335.1_ASM2422633v1_genomic.fna.gz --refList GCA_024226335.1_ASM2422633v1_genomic.fna/target_genomes_gtdb.txt --output GCA_024226335.1_ASM2422633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:56:58,650] [INFO] Task succeeded: fastANI
[2023-06-30 20:56:58,657] [INFO] Found 6 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-30 20:56:58,657] [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
GCA_016875225.1	s__VGRW01 sp016875225	76.5776	160	1667	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__VGRW01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004356455.1	s__SMWZ01 sp004356455	75.5961	70	1667	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__SMWZ01	95.0	99.36	99.36	0.81	0.81	2	-
GCA_003247575.1	s__SZUA-336 sp003247575	75.4357	62	1667	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__SZUA-336;f__SZUA-336;g__SZUA-336	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011055735.1	s__DSOP01 sp011055735	75.1884	65	1667	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__DSOP01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016875395.1	s__VGRF01 sp016875395	75.1595	82	1667	d__Bacteria;p__Myxococcota_A;c__UBA9160;o__UBA9160;f__UBA6930;g__VGRF01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_011526585.1	s__WYBB01 sp011526585	74.8374	56	1667	d__Bacteria;p__Myxococcota;c__UBA9042;o__PHBI01;f__PHBI01;g__WYBB01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:56:58,659] [INFO] GTDB search result was written to GCA_024226335.1_ASM2422633v1_genomic.fna/result_gtdb.tsv
[2023-06-30 20:56:58,659] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:56:58,672] [INFO] DFAST_QC result json was written to GCA_024226335.1_ASM2422633v1_genomic.fna/dqc_result.json
[2023-06-30 20:56:58,672] [INFO] DFAST_QC completed!
[2023-06-30 20:56:58,673] [INFO] Total running time: 0h1m37s