[2023-06-18 17:50:58,822] [INFO] DFAST_QC pipeline started.
[2023-06-18 17:50:58,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-18 17:50:58,825] [INFO] DQC Reference Directory: /var/lib/cwl/stgbee635d8-8626-4865-a20f-63e79050ba1b/dqc_reference
[2023-06-18 17:51:00,024] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-18 17:51:00,025] [INFO] Task started: Prodigal
[2023-06-18 17:51:00,025] [INFO] Running command: gunzip -c /var/lib/cwl/stgb8d70b08-920e-495d-b0e9-ea37bfdab7b6/GCA_013178155.1_ASM1317815v1_genomic.fna.gz | prodigal -d GCA_013178155.1_ASM1317815v1_genomic.fna/cds.fna -a GCA_013178155.1_ASM1317815v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-18 17:51:15,979] [INFO] Task succeeded: Prodigal
[2023-06-18 17:51:15,980] [INFO] Task started: HMMsearch
[2023-06-18 17:51:15,980] [INFO] Running command: hmmsearch --tblout GCA_013178155.1_ASM1317815v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbee635d8-8626-4865-a20f-63e79050ba1b/dqc_reference/reference_markers.hmm GCA_013178155.1_ASM1317815v1_genomic.fna/protein.faa > /dev/null
[2023-06-18 17:51:16,270] [INFO] Task succeeded: HMMsearch
[2023-06-18 17:51:16,271] [INFO] Found 6/6 markers.
[2023-06-18 17:51:16,332] [INFO] Query marker FASTA was written to GCA_013178155.1_ASM1317815v1_genomic.fna/markers.fasta
[2023-06-18 17:51:16,332] [INFO] Task started: Blastn
[2023-06-18 17:51:16,333] [INFO] Running command: blastn -query GCA_013178155.1_ASM1317815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbee635d8-8626-4865-a20f-63e79050ba1b/dqc_reference/reference_markers.fasta -out GCA_013178155.1_ASM1317815v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:51:16,921] [INFO] Task succeeded: Blastn
[2023-06-18 17:51:16,928] [INFO] Selected 20 target genomes.
[2023-06-18 17:51:16,928] [INFO] Target genome list was writen to GCA_013178155.1_ASM1317815v1_genomic.fna/target_genomes.txt
[2023-06-18 17:51:16,930] [INFO] Task started: fastANI
[2023-06-18 17:51:16,930] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d70b08-920e-495d-b0e9-ea37bfdab7b6/GCA_013178155.1_ASM1317815v1_genomic.fna.gz --refList GCA_013178155.1_ASM1317815v1_genomic.fna/target_genomes.txt --output GCA_013178155.1_ASM1317815v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-18 17:51:30,224] [INFO] Task succeeded: fastANI
[2023-06-18 17:51:30,225] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbee635d8-8626-4865-a20f-63e79050ba1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-18 17:51:30,225] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbee635d8-8626-4865-a20f-63e79050ba1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-18 17:51:30,231] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-18 17:51:30,231] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-18 17:51:30,232] [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
Streptomyces palmae	strain=JCM 31289	GCA_004684805.1	1701085	1701085	type	True	74.7865	55	1736	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-18 17:51:30,234] [INFO] DFAST Taxonomy check result was written to GCA_013178155.1_ASM1317815v1_genomic.fna/tc_result.tsv
[2023-06-18 17:51:30,235] [INFO] ===== Taxonomy check completed =====
[2023-06-18 17:51:30,235] [INFO] ===== Start completeness check using CheckM =====
[2023-06-18 17:51:30,235] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbee635d8-8626-4865-a20f-63e79050ba1b/dqc_reference/checkm_data
[2023-06-18 17:51:30,236] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-18 17:51:30,285] [INFO] Task started: CheckM
[2023-06-18 17:51:30,286] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_013178155.1_ASM1317815v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_013178155.1_ASM1317815v1_genomic.fna/checkm_input GCA_013178155.1_ASM1317815v1_genomic.fna/checkm_result
[2023-06-18 17:52:17,355] [INFO] Task succeeded: CheckM
[2023-06-18 17:52:17,357] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 3.47%
Strain heterogeneity: 66.67%
--------------------------------------------------------------------------------
[2023-06-18 17:52:17,394] [INFO] ===== Completeness check finished =====
[2023-06-18 17:52:17,394] [INFO] ===== Start GTDB Search =====
[2023-06-18 17:52:17,395] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_013178155.1_ASM1317815v1_genomic.fna/markers.fasta)
[2023-06-18 17:52:17,395] [INFO] Task started: Blastn
[2023-06-18 17:52:17,395] [INFO] Running command: blastn -query GCA_013178155.1_ASM1317815v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbee635d8-8626-4865-a20f-63e79050ba1b/dqc_reference/reference_markers_gtdb.fasta -out GCA_013178155.1_ASM1317815v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-18 17:52:18,216] [INFO] Task succeeded: Blastn
[2023-06-18 17:52:18,220] [INFO] Selected 19 target genomes.
[2023-06-18 17:52:18,220] [INFO] Target genome list was writen to GCA_013178155.1_ASM1317815v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-18 17:52:18,259] [INFO] Task started: fastANI
[2023-06-18 17:52:18,259] [INFO] Running command: fastANI --query /var/lib/cwl/stgb8d70b08-920e-495d-b0e9-ea37bfdab7b6/GCA_013178155.1_ASM1317815v1_genomic.fna.gz --refList GCA_013178155.1_ASM1317815v1_genomic.fna/target_genomes_gtdb.txt --output GCA_013178155.1_ASM1317815v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-18 17:52:31,453] [INFO] Task succeeded: fastANI
[2023-06-18 17:52:31,459] [INFO] Found 4 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-18 17:52:31,459] [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_013178155.1	s__JABLXH01 sp013178155	100.0	1722	1736	d__Bacteria;p__Armatimonadota;c__UBA5377;o__UBA5377;f__JABLXH01;g__JABLXH01	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_018056145.1	s__JABUFB01 sp018056145	75.8956	124	1736	d__Bacteria;p__Armatimonadota;c__UBA5377;o__UBA5377;f__JABUFB01;g__JABUFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013314775.1	s__JABUFB01 sp013314775	75.8485	112	1736	d__Bacteria;p__Armatimonadota;c__UBA5377;o__UBA5377;f__JABUFB01;g__JABUFB01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016869045.1	s__VGFC01 sp016869045	75.7058	138	1736	d__Bacteria;p__Armatimonadota;c__UBA5377;o__UBA5377;f__VGFC01;g__VGFC01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-18 17:52:31,462] [INFO] GTDB search result was written to GCA_013178155.1_ASM1317815v1_genomic.fna/result_gtdb.tsv
[2023-06-18 17:52:31,462] [INFO] ===== GTDB Search completed =====
[2023-06-18 17:52:31,468] [INFO] DFAST_QC result json was written to GCA_013178155.1_ASM1317815v1_genomic.fna/dqc_result.json
[2023-06-18 17:52:31,468] [INFO] DFAST_QC completed!
[2023-06-18 17:52:31,469] [INFO] Total running time: 0h1m33s