[2023-06-30 05:01:33,050] [INFO] DFAST_QC pipeline started.
[2023-06-30 05:01:33,052] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 05:01:33,052] [INFO] DQC Reference Directory: /var/lib/cwl/stg2fe9392c-b050-4efc-8c23-84ebc137a805/dqc_reference
[2023-06-30 05:01:34,193] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 05:01:34,194] [INFO] Task started: Prodigal
[2023-06-30 05:01:34,194] [INFO] Running command: gunzip -c /var/lib/cwl/stgb6f1349f-a996-4b0f-815d-68ed87cc79d3/GCA_016718975.1_ASM1671897v1_genomic.fna.gz | prodigal -d GCA_016718975.1_ASM1671897v1_genomic.fna/cds.fna -a GCA_016718975.1_ASM1671897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 05:01:47,310] [INFO] Task succeeded: Prodigal
[2023-06-30 05:01:47,310] [INFO] Task started: HMMsearch
[2023-06-30 05:01:47,310] [INFO] Running command: hmmsearch --tblout GCA_016718975.1_ASM1671897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2fe9392c-b050-4efc-8c23-84ebc137a805/dqc_reference/reference_markers.hmm GCA_016718975.1_ASM1671897v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 05:01:47,532] [INFO] Task succeeded: HMMsearch
[2023-06-30 05:01:47,533] [INFO] Found 6/6 markers.
[2023-06-30 05:01:47,566] [INFO] Query marker FASTA was written to GCA_016718975.1_ASM1671897v1_genomic.fna/markers.fasta
[2023-06-30 05:01:47,566] [INFO] Task started: Blastn
[2023-06-30 05:01:47,566] [INFO] Running command: blastn -query GCA_016718975.1_ASM1671897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fe9392c-b050-4efc-8c23-84ebc137a805/dqc_reference/reference_markers.fasta -out GCA_016718975.1_ASM1671897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:01:48,126] [INFO] Task succeeded: Blastn
[2023-06-30 05:01:48,130] [INFO] Selected 19 target genomes.
[2023-06-30 05:01:48,131] [INFO] Target genome list was writen to GCA_016718975.1_ASM1671897v1_genomic.fna/target_genomes.txt
[2023-06-30 05:01:48,134] [INFO] Task started: fastANI
[2023-06-30 05:01:48,134] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f1349f-a996-4b0f-815d-68ed87cc79d3/GCA_016718975.1_ASM1671897v1_genomic.fna.gz --refList GCA_016718975.1_ASM1671897v1_genomic.fna/target_genomes.txt --output GCA_016718975.1_ASM1671897v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 05:01:57,592] [INFO] Task succeeded: fastANI
[2023-06-30 05:01:57,592] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2fe9392c-b050-4efc-8c23-84ebc137a805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 05:01:57,592] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2fe9392c-b050-4efc-8c23-84ebc137a805/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 05:01:57,594] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 05:01:57,594] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 05:01:57,594] [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
--------------------------------------------------------------------------------
[2023-06-30 05:01:57,597] [INFO] DFAST Taxonomy check result was written to GCA_016718975.1_ASM1671897v1_genomic.fna/tc_result.tsv
[2023-06-30 05:01:57,597] [INFO] ===== Taxonomy check completed =====
[2023-06-30 05:01:57,597] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 05:01:57,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2fe9392c-b050-4efc-8c23-84ebc137a805/dqc_reference/checkm_data
[2023-06-30 05:01:57,600] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 05:01:57,639] [INFO] Task started: CheckM
[2023-06-30 05:01:57,640] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016718975.1_ASM1671897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016718975.1_ASM1671897v1_genomic.fna/checkm_input GCA_016718975.1_ASM1671897v1_genomic.fna/checkm_result
[2023-06-30 05:02:39,512] [INFO] Task succeeded: CheckM
[2023-06-30 05:02:39,513] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 05:02:39,531] [INFO] ===== Completeness check finished =====
[2023-06-30 05:02:39,531] [INFO] ===== Start GTDB Search =====
[2023-06-30 05:02:39,532] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016718975.1_ASM1671897v1_genomic.fna/markers.fasta)
[2023-06-30 05:02:39,532] [INFO] Task started: Blastn
[2023-06-30 05:02:39,532] [INFO] Running command: blastn -query GCA_016718975.1_ASM1671897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2fe9392c-b050-4efc-8c23-84ebc137a805/dqc_reference/reference_markers_gtdb.fasta -out GCA_016718975.1_ASM1671897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 05:02:40,330] [INFO] Task succeeded: Blastn
[2023-06-30 05:02:40,333] [INFO] Selected 11 target genomes.
[2023-06-30 05:02:40,333] [INFO] Target genome list was writen to GCA_016718975.1_ASM1671897v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 05:02:40,338] [INFO] Task started: fastANI
[2023-06-30 05:02:40,338] [INFO] Running command: fastANI --query /var/lib/cwl/stgb6f1349f-a996-4b0f-815d-68ed87cc79d3/GCA_016718975.1_ASM1671897v1_genomic.fna.gz --refList GCA_016718975.1_ASM1671897v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016718975.1_ASM1671897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 05:02:48,560] [INFO] Task succeeded: fastANI
[2023-06-30 05:02:48,568] [INFO] Found 9 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 05:02:48,569] [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_016709315.1	s__JAEUSI01 sp016709315	98.8513	1262	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAEUSI01	95.0	98.01	96.43	0.90	0.86	8	conclusive
GCA_018266895.1	s__JAEUSI01 sp018266895	82.8923	822	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAEUSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016719565.1	s__UBA2330 sp016719565	77.1053	321	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__UBA2330	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016788375.1	s__JAEUSI01 sp016788375	77.0689	344	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAEUSI01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266875.1	s__UBA2330 sp018266875	76.7017	216	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__UBA2330	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016716125.1	s__UBA2330 sp016716125	76.6511	260	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__UBA2330	95.0	N/A	N/A	N/A	N/A	1	-
GCA_002344965.1	s__UBA2330 sp002344965	76.4491	228	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__UBA2330	95.0	99.89	99.88	0.93	0.88	3	-
GCA_016218085.1	s__FEN-1279 sp016218085	75.4582	59	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__FEN-1279	95.0	N/A	N/A	N/A	N/A	1	-
GCA_018266835.1	s__JAFDZO01 sp018266835	75.3621	99	1414	d__Bacteria;p__Bacteroidota;c__Ignavibacteria;o__SJA-28;f__B-1AR;g__JAFDZO01	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 05:02:48,570] [INFO] GTDB search result was written to GCA_016718975.1_ASM1671897v1_genomic.fna/result_gtdb.tsv
[2023-06-30 05:02:48,571] [INFO] ===== GTDB Search completed =====
[2023-06-30 05:02:48,573] [INFO] DFAST_QC result json was written to GCA_016718975.1_ASM1671897v1_genomic.fna/dqc_result.json
[2023-06-30 05:02:48,573] [INFO] DFAST_QC completed!
[2023-06-30 05:02:48,573] [INFO] Total running time: 0h1m16s