[2023-07-01 03:09:47,701] [INFO] DFAST_QC pipeline started.
[2023-07-01 03:09:47,704] [INFO] DFAST_QC version: 0.5.7
[2023-07-01 03:09:47,704] [INFO] DQC Reference Directory: /var/lib/cwl/stgf4c1507e-ab29-4434-9ca2-69b92b2a4f75/dqc_reference
[2023-07-01 03:09:48,941] [INFO] ===== Start taxonomy check using ANI =====
[2023-07-01 03:09:48,942] [INFO] Task started: Prodigal
[2023-07-01 03:09:48,943] [INFO] Running command: gunzip -c /var/lib/cwl/stgf207af62-2a88-485f-903a-e76bce387d15/GCA_016716335.1_ASM1671633v1_genomic.fna.gz | prodigal -d GCA_016716335.1_ASM1671633v1_genomic.fna/cds.fna -a GCA_016716335.1_ASM1671633v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-07-01 03:10:08,305] [INFO] Task succeeded: Prodigal
[2023-07-01 03:10:08,306] [INFO] Task started: HMMsearch
[2023-07-01 03:10:08,306] [INFO] Running command: hmmsearch --tblout GCA_016716335.1_ASM1671633v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgf4c1507e-ab29-4434-9ca2-69b92b2a4f75/dqc_reference/reference_markers.hmm GCA_016716335.1_ASM1671633v1_genomic.fna/protein.faa > /dev/null
[2023-07-01 03:10:08,562] [INFO] Task succeeded: HMMsearch
[2023-07-01 03:10:08,563] [INFO] Found 6/6 markers.
[2023-07-01 03:10:08,597] [INFO] Query marker FASTA was written to GCA_016716335.1_ASM1671633v1_genomic.fna/markers.fasta
[2023-07-01 03:10:08,597] [INFO] Task started: Blastn
[2023-07-01 03:10:08,597] [INFO] Running command: blastn -query GCA_016716335.1_ASM1671633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c1507e-ab29-4434-9ca2-69b92b2a4f75/dqc_reference/reference_markers.fasta -out GCA_016716335.1_ASM1671633v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:10:09,170] [INFO] Task succeeded: Blastn
[2023-07-01 03:10:09,175] [INFO] Selected 23 target genomes.
[2023-07-01 03:10:09,176] [INFO] Target genome list was writen to GCA_016716335.1_ASM1671633v1_genomic.fna/target_genomes.txt
[2023-07-01 03:10:09,180] [INFO] Task started: fastANI
[2023-07-01 03:10:09,180] [INFO] Running command: fastANI --query /var/lib/cwl/stgf207af62-2a88-485f-903a-e76bce387d15/GCA_016716335.1_ASM1671633v1_genomic.fna.gz --refList GCA_016716335.1_ASM1671633v1_genomic.fna/target_genomes.txt --output GCA_016716335.1_ASM1671633v1_genomic.fna/fastani_result.tsv --threads 1
[2023-07-01 03:10:23,735] [INFO] Task succeeded: fastANI
[2023-07-01 03:10:23,736] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgf4c1507e-ab29-4434-9ca2-69b92b2a4f75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-07-01 03:10:23,736] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgf4c1507e-ab29-4434-9ca2-69b92b2a4f75/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-07-01 03:10:23,738] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-07-01 03:10:23,738] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-07-01 03:10:23,738] [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
--------------------------------------------------------------------------------
[2023-07-01 03:10:23,741] [INFO] DFAST Taxonomy check result was written to GCA_016716335.1_ASM1671633v1_genomic.fna/tc_result.tsv
[2023-07-01 03:10:23,741] [INFO] ===== Taxonomy check completed =====
[2023-07-01 03:10:23,741] [INFO] ===== Start completeness check using CheckM =====
[2023-07-01 03:10:23,742] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgf4c1507e-ab29-4434-9ca2-69b92b2a4f75/dqc_reference/checkm_data
[2023-07-01 03:10:23,745] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-07-01 03:10:23,788] [INFO] Task started: CheckM
[2023-07-01 03:10:23,788] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016716335.1_ASM1671633v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016716335.1_ASM1671633v1_genomic.fna/checkm_input GCA_016716335.1_ASM1671633v1_genomic.fna/checkm_result
[2023-07-01 03:11:21,976] [INFO] Task succeeded: CheckM
[2023-07-01 03:11:21,978] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-07-01 03:11:22,000] [INFO] ===== Completeness check finished =====
[2023-07-01 03:11:22,000] [INFO] ===== Start GTDB Search =====
[2023-07-01 03:11:22,000] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016716335.1_ASM1671633v1_genomic.fna/markers.fasta)
[2023-07-01 03:11:22,001] [INFO] Task started: Blastn
[2023-07-01 03:11:22,001] [INFO] Running command: blastn -query GCA_016716335.1_ASM1671633v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgf4c1507e-ab29-4434-9ca2-69b92b2a4f75/dqc_reference/reference_markers_gtdb.fasta -out GCA_016716335.1_ASM1671633v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-07-01 03:11:22,740] [INFO] Task succeeded: Blastn
[2023-07-01 03:11:22,745] [INFO] Selected 33 target genomes.
[2023-07-01 03:11:22,745] [INFO] Target genome list was writen to GCA_016716335.1_ASM1671633v1_genomic.fna/target_genomes_gtdb.txt
[2023-07-01 03:11:22,763] [INFO] Task started: fastANI
[2023-07-01 03:11:22,764] [INFO] Running command: fastANI --query /var/lib/cwl/stgf207af62-2a88-485f-903a-e76bce387d15/GCA_016716335.1_ASM1671633v1_genomic.fna.gz --refList GCA_016716335.1_ASM1671633v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016716335.1_ASM1671633v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-07-01 03:11:44,374] [INFO] Task succeeded: fastANI
[2023-07-01 03:11:44,388] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2023-07-01 03:11:44,389] [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_016716335.1	s__OLB9 sp016716335	100.0	1323	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_016715985.1	s__OLB9 sp016715985	77.2722	124	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714895.1	s__OLB9 sp016714895	77.1228	52	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016714765.1	s__OLB9 sp016714765	76.6464	63	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	99.01	98.87	0.88	0.87	3	-
GCA_016715245.1	s__OLB9 sp016715245	76.6313	57	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	99.11	98.72	0.92	0.89	11	-
GCA_016714445.1	s__OLB9 sp016714445	76.4538	84	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	97.58	97.50	0.85	0.84	3	-
GCA_019136675.1	s__OLB9 sp019136675	75.8407	53	1323	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Chitinophagales;f__Saprospiraceae;g__OLB9	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-07-01 03:11:44,406] [INFO] GTDB search result was written to GCA_016716335.1_ASM1671633v1_genomic.fna/result_gtdb.tsv
[2023-07-01 03:11:44,407] [INFO] ===== GTDB Search completed =====
[2023-07-01 03:11:44,409] [INFO] DFAST_QC result json was written to GCA_016716335.1_ASM1671633v1_genomic.fna/dqc_result.json
[2023-07-01 03:11:44,410] [INFO] DFAST_QC completed!
[2023-07-01 03:11:44,410] [INFO] Total running time: 0h1m57s