[2023-06-29 04:01:18,823] [INFO] DFAST_QC pipeline started.
[2023-06-29 04:01:18,825] [INFO] DFAST_QC version: 0.5.7
[2023-06-29 04:01:18,826] [INFO] DQC Reference Directory: /var/lib/cwl/stg26926aaa-caeb-46e1-b037-b043ad17f833/dqc_reference
[2023-06-29 04:01:20,276] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-29 04:01:20,277] [INFO] Task started: Prodigal
[2023-06-29 04:01:20,278] [INFO] Running command: gunzip -c /var/lib/cwl/stgd0936720-25e9-434e-b334-2fd347d68c03/GCA_020062175.1_ASM2006217v1_genomic.fna.gz | prodigal -d GCA_020062175.1_ASM2006217v1_genomic.fna/cds.fna -a GCA_020062175.1_ASM2006217v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-29 04:01:24,372] [INFO] Task succeeded: Prodigal
[2023-06-29 04:01:24,373] [INFO] Task started: HMMsearch
[2023-06-29 04:01:24,374] [INFO] Running command: hmmsearch --tblout GCA_020062175.1_ASM2006217v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg26926aaa-caeb-46e1-b037-b043ad17f833/dqc_reference/reference_markers.hmm GCA_020062175.1_ASM2006217v1_genomic.fna/protein.faa > /dev/null
[2023-06-29 04:01:24,717] [INFO] Task succeeded: HMMsearch
[2023-06-29 04:01:24,720] [INFO] Found 6/6 markers.
[2023-06-29 04:01:24,760] [INFO] Query marker FASTA was written to GCA_020062175.1_ASM2006217v1_genomic.fna/markers.fasta
[2023-06-29 04:01:24,761] [INFO] Task started: Blastn
[2023-06-29 04:01:24,761] [INFO] Running command: blastn -query GCA_020062175.1_ASM2006217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26926aaa-caeb-46e1-b037-b043ad17f833/dqc_reference/reference_markers.fasta -out GCA_020062175.1_ASM2006217v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:01:25,570] [INFO] Task succeeded: Blastn
[2023-06-29 04:01:25,574] [INFO] Selected 13 target genomes.
[2023-06-29 04:01:25,575] [INFO] Target genome list was writen to GCA_020062175.1_ASM2006217v1_genomic.fna/target_genomes.txt
[2023-06-29 04:01:25,589] [INFO] Task started: fastANI
[2023-06-29 04:01:25,589] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0936720-25e9-434e-b334-2fd347d68c03/GCA_020062175.1_ASM2006217v1_genomic.fna.gz --refList GCA_020062175.1_ASM2006217v1_genomic.fna/target_genomes.txt --output GCA_020062175.1_ASM2006217v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-29 04:01:34,791] [INFO] Task succeeded: fastANI
[2023-06-29 04:01:34,791] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg26926aaa-caeb-46e1-b037-b043ad17f833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-29 04:01:34,792] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg26926aaa-caeb-46e1-b037-b043ad17f833/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-29 04:01:34,794] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-29 04:01:34,794] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-29 04:01:34,794] [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
--------------------------------------------------------------------------------
[2023-06-29 04:01:34,798] [INFO] DFAST Taxonomy check result was written to GCA_020062175.1_ASM2006217v1_genomic.fna/tc_result.tsv
[2023-06-29 04:01:34,799] [INFO] ===== Taxonomy check completed =====
[2023-06-29 04:01:34,799] [INFO] ===== Start completeness check using CheckM =====
[2023-06-29 04:01:34,800] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg26926aaa-caeb-46e1-b037-b043ad17f833/dqc_reference/checkm_data
[2023-06-29 04:01:34,803] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-29 04:01:34,827] [INFO] Task started: CheckM
[2023-06-29 04:01:34,827] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020062175.1_ASM2006217v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020062175.1_ASM2006217v1_genomic.fna/checkm_input GCA_020062175.1_ASM2006217v1_genomic.fna/checkm_result
[2023-06-29 04:01:55,277] [INFO] Task succeeded: CheckM
[2023-06-29 04:01:55,281] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 68.94%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-29 04:01:55,313] [INFO] ===== Completeness check finished =====
[2023-06-29 04:01:55,314] [INFO] ===== Start GTDB Search =====
[2023-06-29 04:01:55,314] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020062175.1_ASM2006217v1_genomic.fna/markers.fasta)
[2023-06-29 04:01:55,315] [INFO] Task started: Blastn
[2023-06-29 04:01:55,315] [INFO] Running command: blastn -query GCA_020062175.1_ASM2006217v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg26926aaa-caeb-46e1-b037-b043ad17f833/dqc_reference/reference_markers_gtdb.fasta -out GCA_020062175.1_ASM2006217v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-29 04:01:56,633] [INFO] Task succeeded: Blastn
[2023-06-29 04:01:56,638] [INFO] Selected 17 target genomes.
[2023-06-29 04:01:56,638] [INFO] Target genome list was writen to GCA_020062175.1_ASM2006217v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-29 04:01:56,652] [INFO] Task started: fastANI
[2023-06-29 04:01:56,652] [INFO] Running command: fastANI --query /var/lib/cwl/stgd0936720-25e9-434e-b334-2fd347d68c03/GCA_020062175.1_ASM2006217v1_genomic.fna.gz --refList GCA_020062175.1_ASM2006217v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020062175.1_ASM2006217v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-29 04:02:07,442] [INFO] Task succeeded: fastANI
[2023-06-29 04:02:07,468] [INFO] Found 9 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-29 04:02:07,469] [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_002780715.1	s__UBA1163 sp002780715	79.037	224	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__UBA1163	95.0	99.21	99.21	0.80	0.80	2	-
GCA_018333535.1	s__RBG-16-49-23 sp018333535	78.3095	136	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002327985.1	s__UBA1163 sp002327985	77.9486	151	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__UBA1163	95.0	99.83	99.83	0.89	0.89	2	-
GCA_002327885.1	s__UBA1163 sp002327885	77.6964	135	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__UBA1163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002311635.1	s__UBA1163 sp002311635	77.5681	101	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__UBA1163	95.0	99.90	99.90	0.85	0.85	2	-
GCA_016875255.1	s__RBG-16-49-23 sp016875255	77.5195	110	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016874935.1	s__RBG-16-49-23 sp016874935	77.2757	101	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__RBG-16-49-23	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388645.1	s__UBA1163 sp013388645	76.971	121	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__UBA1163	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013388635.1	s__JACAEX01 sp013388635	76.586	126	466	d__Bacteria;p__Desulfobacterota;c__BSN033;o__BSN033;f__UBA1163;g__JACAEX01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-29 04:02:07,471] [INFO] GTDB search result was written to GCA_020062175.1_ASM2006217v1_genomic.fna/result_gtdb.tsv
[2023-06-29 04:02:07,473] [INFO] ===== GTDB Search completed =====
[2023-06-29 04:02:07,477] [INFO] DFAST_QC result json was written to GCA_020062175.1_ASM2006217v1_genomic.fna/dqc_result.json
[2023-06-29 04:02:07,477] [INFO] DFAST_QC completed!
[2023-06-29 04:02:07,477] [INFO] Total running time: 0h0m49s