[2023-06-13 13:00:23,718] [INFO] DFAST_QC pipeline started.
[2023-06-13 13:00:23,723] [INFO] DFAST_QC version: 0.5.7
[2023-06-13 13:00:23,724] [INFO] DQC Reference Directory: /var/lib/cwl/stg84566bd6-a90d-4c0a-b37a-ae26e12ae92b/dqc_reference
[2023-06-13 13:00:24,986] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-13 13:00:24,987] [INFO] Task started: Prodigal
[2023-06-13 13:00:24,987] [INFO] Running command: gunzip -c /var/lib/cwl/stg820e864d-6f50-4e52-a5b6-d033ab8739e9/GCA_022704565.1_ASM2270456v1_genomic.fna.gz | prodigal -d GCA_022704565.1_ASM2270456v1_genomic.fna/cds.fna -a GCA_022704565.1_ASM2270456v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-13 13:00:32,607] [INFO] Task succeeded: Prodigal
[2023-06-13 13:00:32,607] [INFO] Task started: HMMsearch
[2023-06-13 13:00:32,607] [INFO] Running command: hmmsearch --tblout GCA_022704565.1_ASM2270456v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg84566bd6-a90d-4c0a-b37a-ae26e12ae92b/dqc_reference/reference_markers.hmm GCA_022704565.1_ASM2270456v1_genomic.fna/protein.faa > /dev/null
[2023-06-13 13:00:32,858] [INFO] Task succeeded: HMMsearch
[2023-06-13 13:00:32,859] [INFO] Found 6/6 markers.
[2023-06-13 13:00:32,890] [INFO] Query marker FASTA was written to GCA_022704565.1_ASM2270456v1_genomic.fna/markers.fasta
[2023-06-13 13:00:32,890] [INFO] Task started: Blastn
[2023-06-13 13:00:32,890] [INFO] Running command: blastn -query GCA_022704565.1_ASM2270456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84566bd6-a90d-4c0a-b37a-ae26e12ae92b/dqc_reference/reference_markers.fasta -out GCA_022704565.1_ASM2270456v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:00:33,530] [INFO] Task succeeded: Blastn
[2023-06-13 13:00:33,534] [INFO] Selected 20 target genomes.
[2023-06-13 13:00:33,535] [INFO] Target genome list was writen to GCA_022704565.1_ASM2270456v1_genomic.fna/target_genomes.txt
[2023-06-13 13:00:33,558] [INFO] Task started: fastANI
[2023-06-13 13:00:33,559] [INFO] Running command: fastANI --query /var/lib/cwl/stg820e864d-6f50-4e52-a5b6-d033ab8739e9/GCA_022704565.1_ASM2270456v1_genomic.fna.gz --refList GCA_022704565.1_ASM2270456v1_genomic.fna/target_genomes.txt --output GCA_022704565.1_ASM2270456v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-13 13:00:45,019] [INFO] Task succeeded: fastANI
[2023-06-13 13:00:45,019] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg84566bd6-a90d-4c0a-b37a-ae26e12ae92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-13 13:00:45,020] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg84566bd6-a90d-4c0a-b37a-ae26e12ae92b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-13 13:00:45,021] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-13 13:00:45,022] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-13 13:00:45,022] [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
--------------------------------------------------------------------------------
[2023-06-13 13:00:45,024] [INFO] DFAST Taxonomy check result was written to GCA_022704565.1_ASM2270456v1_genomic.fna/tc_result.tsv
[2023-06-13 13:00:45,025] [INFO] ===== Taxonomy check completed =====
[2023-06-13 13:00:45,025] [INFO] ===== Start completeness check using CheckM =====
[2023-06-13 13:00:45,025] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg84566bd6-a90d-4c0a-b37a-ae26e12ae92b/dqc_reference/checkm_data
[2023-06-13 13:00:45,028] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-13 13:00:45,064] [INFO] Task started: CheckM
[2023-06-13 13:00:45,064] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_022704565.1_ASM2270456v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_022704565.1_ASM2270456v1_genomic.fna/checkm_input GCA_022704565.1_ASM2270456v1_genomic.fna/checkm_result
[2023-06-13 13:01:12,517] [INFO] Task succeeded: CheckM
[2023-06-13 13:01:12,518] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 87.50%
Contamintation: 0.52%
Strain heterogeneity: 100.00%
--------------------------------------------------------------------------------
[2023-06-13 13:01:12,541] [INFO] ===== Completeness check finished =====
[2023-06-13 13:01:12,541] [INFO] ===== Start GTDB Search =====
[2023-06-13 13:01:12,541] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_022704565.1_ASM2270456v1_genomic.fna/markers.fasta)
[2023-06-13 13:01:12,542] [INFO] Task started: Blastn
[2023-06-13 13:01:12,542] [INFO] Running command: blastn -query GCA_022704565.1_ASM2270456v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg84566bd6-a90d-4c0a-b37a-ae26e12ae92b/dqc_reference/reference_markers_gtdb.fasta -out GCA_022704565.1_ASM2270456v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-13 13:01:13,377] [INFO] Task succeeded: Blastn
[2023-06-13 13:01:13,386] [INFO] Selected 13 target genomes.
[2023-06-13 13:01:13,386] [INFO] Target genome list was writen to GCA_022704565.1_ASM2270456v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-13 13:01:13,394] [INFO] Task started: fastANI
[2023-06-13 13:01:13,394] [INFO] Running command: fastANI --query /var/lib/cwl/stg820e864d-6f50-4e52-a5b6-d033ab8739e9/GCA_022704565.1_ASM2270456v1_genomic.fna.gz --refList GCA_022704565.1_ASM2270456v1_genomic.fna/target_genomes_gtdb.txt --output GCA_022704565.1_ASM2270456v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-13 13:01:20,774] [INFO] Task succeeded: fastANI
[2023-06-13 13:01:20,786] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-13 13:01:20,786] [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_002069125.1	s__MVZN01 sp002069125	99.6809	830	918	d__Bacteria;p__Spirochaetota;c__UBA4802;o__UBA4802;f__UBA5368;g__MVZN01	95.0	99.52	99.52	0.94	0.94	2	conclusive
GCA_017998475.1	s__MVZN01 sp017998475	81.6822	509	918	d__Bacteria;p__Spirochaetota;c__UBA4802;o__UBA4802;f__UBA5368;g__MVZN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018263175.1	s__MVZN01 sp018263175	78.7371	335	918	d__Bacteria;p__Spirochaetota;c__UBA4802;o__UBA4802;f__UBA5368;g__MVZN01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_004297825.1	s__FW300-bin19 sp004297825	76.4741	92	918	d__Bacteria;p__Spirochaetota;c__UBA4802;o__UBA4802;f__UBA5368;g__FW300-bin19	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002407865.1	s__UBA5368 sp002407865	76.2132	66	918	d__Bacteria;p__Spirochaetota;c__UBA4802;o__UBA4802;f__UBA5368;g__UBA5368	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-13 13:01:20,789] [INFO] GTDB search result was written to GCA_022704565.1_ASM2270456v1_genomic.fna/result_gtdb.tsv
[2023-06-13 13:01:20,790] [INFO] ===== GTDB Search completed =====
[2023-06-13 13:01:20,793] [INFO] DFAST_QC result json was written to GCA_022704565.1_ASM2270456v1_genomic.fna/dqc_result.json
[2023-06-13 13:01:20,794] [INFO] DFAST_QC completed!
[2023-06-13 13:01:20,794] [INFO] Total running time: 0h0m57s