[2023-06-28 17:00:52,340] [INFO] DFAST_QC pipeline started.
[2023-06-28 17:00:52,345] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 17:00:52,345] [INFO] DQC Reference Directory: /var/lib/cwl/stg419b441b-b644-4e0d-8838-0100670b8153/dqc_reference
[2023-06-28 17:00:53,627] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 17:00:53,628] [INFO] Task started: Prodigal
[2023-06-28 17:00:53,628] [INFO] Running command: gunzip -c /var/lib/cwl/stgdcf9835a-0c79-4f5e-b2ca-05dabb6b4899/GCA_027344545.1_ASM2734454v1_genomic.fna.gz | prodigal -d GCA_027344545.1_ASM2734454v1_genomic.fna/cds.fna -a GCA_027344545.1_ASM2734454v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 17:00:58,008] [INFO] Task succeeded: Prodigal
[2023-06-28 17:00:58,009] [INFO] Task started: HMMsearch
[2023-06-28 17:00:58,009] [INFO] Running command: hmmsearch --tblout GCA_027344545.1_ASM2734454v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg419b441b-b644-4e0d-8838-0100670b8153/dqc_reference/reference_markers.hmm GCA_027344545.1_ASM2734454v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 17:00:58,254] [INFO] Task succeeded: HMMsearch
[2023-06-28 17:00:58,255] [INFO] Found 6/6 markers.
[2023-06-28 17:00:58,275] [INFO] Query marker FASTA was written to GCA_027344545.1_ASM2734454v1_genomic.fna/markers.fasta
[2023-06-28 17:00:58,275] [INFO] Task started: Blastn
[2023-06-28 17:00:58,275] [INFO] Running command: blastn -query GCA_027344545.1_ASM2734454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg419b441b-b644-4e0d-8838-0100670b8153/dqc_reference/reference_markers.fasta -out GCA_027344545.1_ASM2734454v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:00:58,969] [INFO] Task succeeded: Blastn
[2023-06-28 17:00:58,973] [INFO] Selected 24 target genomes.
[2023-06-28 17:00:58,973] [INFO] Target genome list was writen to GCA_027344545.1_ASM2734454v1_genomic.fna/target_genomes.txt
[2023-06-28 17:00:58,980] [INFO] Task started: fastANI
[2023-06-28 17:00:58,981] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf9835a-0c79-4f5e-b2ca-05dabb6b4899/GCA_027344545.1_ASM2734454v1_genomic.fna.gz --refList GCA_027344545.1_ASM2734454v1_genomic.fna/target_genomes.txt --output GCA_027344545.1_ASM2734454v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 17:01:16,519] [INFO] Task succeeded: fastANI
[2023-06-28 17:01:16,520] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg419b441b-b644-4e0d-8838-0100670b8153/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 17:01:16,520] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg419b441b-b644-4e0d-8838-0100670b8153/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 17:01:16,525] [INFO] Found 2 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 17:01:16,526] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 17:01:16,526] [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
Tistlia consotensis	strain=DSM 21585	GCA_900188055.1	1321365	1321365	type	True	75.0786	66	489	95	below_threshold
Tistlia consotensis	strain=USBA 355	GCA_900177295.1	1321365	1321365	type	True	75.0644	68	489	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 17:01:16,528] [INFO] DFAST Taxonomy check result was written to GCA_027344545.1_ASM2734454v1_genomic.fna/tc_result.tsv
[2023-06-28 17:01:16,529] [INFO] ===== Taxonomy check completed =====
[2023-06-28 17:01:16,529] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 17:01:16,529] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg419b441b-b644-4e0d-8838-0100670b8153/dqc_reference/checkm_data
[2023-06-28 17:01:16,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 17:01:16,550] [INFO] Task started: CheckM
[2023-06-28 17:01:16,550] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_027344545.1_ASM2734454v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_027344545.1_ASM2734454v1_genomic.fna/checkm_input GCA_027344545.1_ASM2734454v1_genomic.fna/checkm_result
[2023-06-28 17:01:36,173] [INFO] Task succeeded: CheckM
[2023-06-28 17:01:36,175] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 17:01:36,195] [INFO] ===== Completeness check finished =====
[2023-06-28 17:01:36,195] [INFO] ===== Start GTDB Search =====
[2023-06-28 17:01:36,195] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_027344545.1_ASM2734454v1_genomic.fna/markers.fasta)
[2023-06-28 17:01:36,196] [INFO] Task started: Blastn
[2023-06-28 17:01:36,196] [INFO] Running command: blastn -query GCA_027344545.1_ASM2734454v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg419b441b-b644-4e0d-8838-0100670b8153/dqc_reference/reference_markers_gtdb.fasta -out GCA_027344545.1_ASM2734454v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 17:01:37,112] [INFO] Task succeeded: Blastn
[2023-06-28 17:01:37,116] [INFO] Selected 25 target genomes.
[2023-06-28 17:01:37,116] [INFO] Target genome list was writen to GCA_027344545.1_ASM2734454v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 17:01:37,136] [INFO] Task started: fastANI
[2023-06-28 17:01:37,136] [INFO] Running command: fastANI --query /var/lib/cwl/stgdcf9835a-0c79-4f5e-b2ca-05dabb6b4899/GCA_027344545.1_ASM2734454v1_genomic.fna.gz --refList GCA_027344545.1_ASM2734454v1_genomic.fna/target_genomes_gtdb.txt --output GCA_027344545.1_ASM2734454v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 17:01:53,957] [INFO] Task succeeded: fastANI
[2023-06-28 17:01:53,988] [INFO] Found 2 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 17:01:53,989] [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_900177295.1	s__Tistlia consotensis	75.0644	68	489	d__Bacteria;p__Proteobacteria;c__Alphaproteobacteria;o__Kiloniellales;f__DSM-21159;g__Tistlia	95.0	99.99	99.99	0.99	0.99	2	-
GCA_016794525.1	s__UBA2376 sp016794525	74.7714	61	489	d__Bacteria;p__Myxococcota;c__Polyangia;o__Haliangiales;f__Haliangiaceae;g__UBA2376	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 17:01:53,991] [INFO] GTDB search result was written to GCA_027344545.1_ASM2734454v1_genomic.fna/result_gtdb.tsv
[2023-06-28 17:01:53,992] [INFO] ===== GTDB Search completed =====
[2023-06-28 17:01:53,996] [INFO] DFAST_QC result json was written to GCA_027344545.1_ASM2734454v1_genomic.fna/dqc_result.json
[2023-06-28 17:01:53,996] [INFO] DFAST_QC completed!
[2023-06-28 17:01:53,996] [INFO] Total running time: 0h1m2s