[2023-06-07 20:07:53,333] [INFO] DFAST_QC pipeline started.
[2023-06-07 20:07:53,341] [INFO] DFAST_QC version: 0.5.7
[2023-06-07 20:07:53,341] [INFO] DQC Reference Directory: /var/lib/cwl/stg198bed8c-52a3-4d0a-a7b6-f5295755b6a4/dqc_reference
[2023-06-07 20:07:54,837] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-07 20:07:54,838] [INFO] Task started: Prodigal
[2023-06-07 20:07:54,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg592e117c-6f1d-479e-b943-01ab088df3f5/GCA_945890585.1_MiE-16apr19-152_genomic.fna.gz | prodigal -d GCA_945890585.1_MiE-16apr19-152_genomic.fna/cds.fna -a GCA_945890585.1_MiE-16apr19-152_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-07 20:08:03,617] [INFO] Task succeeded: Prodigal
[2023-06-07 20:08:03,617] [INFO] Task started: HMMsearch
[2023-06-07 20:08:03,618] [INFO] Running command: hmmsearch --tblout GCA_945890585.1_MiE-16apr19-152_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg198bed8c-52a3-4d0a-a7b6-f5295755b6a4/dqc_reference/reference_markers.hmm GCA_945890585.1_MiE-16apr19-152_genomic.fna/protein.faa > /dev/null
[2023-06-07 20:08:03,881] [INFO] Task succeeded: HMMsearch
[2023-06-07 20:08:03,883] [WARNING] Found 5/6 markers. [/var/lib/cwl/stg592e117c-6f1d-479e-b943-01ab088df3f5/GCA_945890585.1_MiE-16apr19-152_genomic.fna.gz]
[2023-06-07 20:08:03,916] [INFO] Query marker FASTA was written to GCA_945890585.1_MiE-16apr19-152_genomic.fna/markers.fasta
[2023-06-07 20:08:03,917] [INFO] Task started: Blastn
[2023-06-07 20:08:03,917] [INFO] Running command: blastn -query GCA_945890585.1_MiE-16apr19-152_genomic.fna/markers.fasta -db /var/lib/cwl/stg198bed8c-52a3-4d0a-a7b6-f5295755b6a4/dqc_reference/reference_markers.fasta -out GCA_945890585.1_MiE-16apr19-152_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:08:04,568] [INFO] Task succeeded: Blastn
[2023-06-07 20:08:04,577] [INFO] Selected 34 target genomes.
[2023-06-07 20:08:04,578] [INFO] Target genome list was writen to GCA_945890585.1_MiE-16apr19-152_genomic.fna/target_genomes.txt
[2023-06-07 20:08:04,594] [INFO] Task started: fastANI
[2023-06-07 20:08:04,594] [INFO] Running command: fastANI --query /var/lib/cwl/stg592e117c-6f1d-479e-b943-01ab088df3f5/GCA_945890585.1_MiE-16apr19-152_genomic.fna.gz --refList GCA_945890585.1_MiE-16apr19-152_genomic.fna/target_genomes.txt --output GCA_945890585.1_MiE-16apr19-152_genomic.fna/fastani_result.tsv --threads 1
[2023-06-07 20:08:30,457] [INFO] Task succeeded: fastANI
[2023-06-07 20:08:30,457] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg198bed8c-52a3-4d0a-a7b6-f5295755b6a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-07 20:08:30,458] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg198bed8c-52a3-4d0a-a7b6-f5295755b6a4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-07 20:08:30,465] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-07 20:08:30,466] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-07 20:08:30,466] [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
Zwartia hollandica	strain=LF4-65	GCA_019923725.1	324606	324606	type	True	78.0397	142	1000	95	below_threshold
Sheuella amnicola	strain=NBD-18	GCA_010499255.1	2707330	2707330	type	True	76.5669	82	1000	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-07 20:08:30,468] [INFO] DFAST Taxonomy check result was written to GCA_945890585.1_MiE-16apr19-152_genomic.fna/tc_result.tsv
[2023-06-07 20:08:30,469] [INFO] ===== Taxonomy check completed =====
[2023-06-07 20:08:30,469] [INFO] ===== Start completeness check using CheckM =====
[2023-06-07 20:08:30,469] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg198bed8c-52a3-4d0a-a7b6-f5295755b6a4/dqc_reference/checkm_data
[2023-06-07 20:08:30,470] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-07 20:08:30,509] [INFO] Task started: CheckM
[2023-06-07 20:08:30,510] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_945890585.1_MiE-16apr19-152_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_945890585.1_MiE-16apr19-152_genomic.fna/checkm_input GCA_945890585.1_MiE-16apr19-152_genomic.fna/checkm_result
[2023-06-07 20:09:02,179] [INFO] Task succeeded: CheckM
[2023-06-07 20:09:02,180] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 58.33%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-07 20:09:02,199] [INFO] ===== Completeness check finished =====
[2023-06-07 20:09:02,199] [INFO] ===== Start GTDB Search =====
[2023-06-07 20:09:02,200] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_945890585.1_MiE-16apr19-152_genomic.fna/markers.fasta)
[2023-06-07 20:09:02,200] [INFO] Task started: Blastn
[2023-06-07 20:09:02,200] [INFO] Running command: blastn -query GCA_945890585.1_MiE-16apr19-152_genomic.fna/markers.fasta -db /var/lib/cwl/stg198bed8c-52a3-4d0a-a7b6-f5295755b6a4/dqc_reference/reference_markers_gtdb.fasta -out GCA_945890585.1_MiE-16apr19-152_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-07 20:09:03,271] [INFO] Task succeeded: Blastn
[2023-06-07 20:09:03,276] [INFO] Selected 30 target genomes.
[2023-06-07 20:09:03,276] [INFO] Target genome list was writen to GCA_945890585.1_MiE-16apr19-152_genomic.fna/target_genomes_gtdb.txt
[2023-06-07 20:09:03,312] [INFO] Task started: fastANI
[2023-06-07 20:09:03,313] [INFO] Running command: fastANI --query /var/lib/cwl/stg592e117c-6f1d-479e-b943-01ab088df3f5/GCA_945890585.1_MiE-16apr19-152_genomic.fna.gz --refList GCA_945890585.1_MiE-16apr19-152_genomic.fna/target_genomes_gtdb.txt --output GCA_945890585.1_MiE-16apr19-152_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-07 20:09:21,874] [INFO] Task succeeded: fastANI
[2023-06-07 20:09:21,889] [INFO] Found 8 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-07 20:09:21,889] [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_002292845.1	s__NBD-18 sp002292845	91.0311	512	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002737415.1	s__NBD-18 sp002737415	77.6067	123	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903903735.1	s__NBD-18 sp903903735	77.2586	107	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903929925.1	s__NBD-18 sp903929925	77.1864	107	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903865015.1	s__NBD-18 sp903865015	76.8884	109	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903924715.1	s__NBD-18 sp903924715	76.68	68	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	N/A	N/A	N/A	N/A	1	-
GCF_010499255.1	s__NBD-18 sp003507735	76.5663	81	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.47	99.47	0.95	0.95	2	-
GCA_903894155.1	s__NBD-18 sp903894155	76.3199	67	1000	d__Bacteria;p__Proteobacteria;c__Gammaproteobacteria;o__Burkholderiales;f__Burkholderiaceae;g__NBD-18	95.0	99.08	98.85	0.85	0.83	4	-
--------------------------------------------------------------------------------
[2023-06-07 20:09:21,890] [INFO] GTDB search result was written to GCA_945890585.1_MiE-16apr19-152_genomic.fna/result_gtdb.tsv
[2023-06-07 20:09:21,891] [INFO] ===== GTDB Search completed =====
[2023-06-07 20:09:21,893] [INFO] DFAST_QC result json was written to GCA_945890585.1_MiE-16apr19-152_genomic.fna/dqc_result.json
[2023-06-07 20:09:21,893] [INFO] DFAST_QC completed!
[2023-06-07 20:09:21,894] [INFO] Total running time: 0h1m29s