[2023-06-30 14:48:14,066] [INFO] DFAST_QC pipeline started.
[2023-06-30 14:48:14,068] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 14:48:14,068] [INFO] DQC Reference Directory: /var/lib/cwl/stg01fa54a5-dc44-4586-80de-01106adbe320/dqc_reference
[2023-06-30 14:48:15,313] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 14:48:15,314] [INFO] Task started: Prodigal
[2023-06-30 14:48:15,314] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ea29a96-050c-482e-82dc-ad4d3e43aa2f/GCA_016708515.1_ASM1670851v1_genomic.fna.gz | prodigal -d GCA_016708515.1_ASM1670851v1_genomic.fna/cds.fna -a GCA_016708515.1_ASM1670851v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 14:48:35,703] [INFO] Task succeeded: Prodigal
[2023-06-30 14:48:35,704] [INFO] Task started: HMMsearch
[2023-06-30 14:48:35,704] [INFO] Running command: hmmsearch --tblout GCA_016708515.1_ASM1670851v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg01fa54a5-dc44-4586-80de-01106adbe320/dqc_reference/reference_markers.hmm GCA_016708515.1_ASM1670851v1_genomic.fna/protein.faa > /dev/null
[2023-06-30 14:48:35,987] [INFO] Task succeeded: HMMsearch
[2023-06-30 14:48:35,988] [INFO] Found 6/6 markers.
[2023-06-30 14:48:36,041] [INFO] Query marker FASTA was written to GCA_016708515.1_ASM1670851v1_genomic.fna/markers.fasta
[2023-06-30 14:48:36,041] [INFO] Task started: Blastn
[2023-06-30 14:48:36,041] [INFO] Running command: blastn -query GCA_016708515.1_ASM1670851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01fa54a5-dc44-4586-80de-01106adbe320/dqc_reference/reference_markers.fasta -out GCA_016708515.1_ASM1670851v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:48:36,652] [INFO] Task succeeded: Blastn
[2023-06-30 14:48:36,657] [INFO] Selected 30 target genomes.
[2023-06-30 14:48:36,658] [INFO] Target genome list was writen to GCA_016708515.1_ASM1670851v1_genomic.fna/target_genomes.txt
[2023-06-30 14:48:36,664] [INFO] Task started: fastANI
[2023-06-30 14:48:36,664] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ea29a96-050c-482e-82dc-ad4d3e43aa2f/GCA_016708515.1_ASM1670851v1_genomic.fna.gz --refList GCA_016708515.1_ASM1670851v1_genomic.fna/target_genomes.txt --output GCA_016708515.1_ASM1670851v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 14:48:53,891] [INFO] Task succeeded: fastANI
[2023-06-30 14:48:53,892] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg01fa54a5-dc44-4586-80de-01106adbe320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 14:48:53,893] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg01fa54a5-dc44-4586-80de-01106adbe320/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 14:48:53,895] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 14:48:53,895] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 14:48:53,895] [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 14:48:53,897] [INFO] DFAST Taxonomy check result was written to GCA_016708515.1_ASM1670851v1_genomic.fna/tc_result.tsv
[2023-06-30 14:48:53,898] [INFO] ===== Taxonomy check completed =====
[2023-06-30 14:48:53,898] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 14:48:53,899] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg01fa54a5-dc44-4586-80de-01106adbe320/dqc_reference/checkm_data
[2023-06-30 14:48:53,902] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 14:48:53,952] [INFO] Task started: CheckM
[2023-06-30 14:48:53,952] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_016708515.1_ASM1670851v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_016708515.1_ASM1670851v1_genomic.fna/checkm_input GCA_016708515.1_ASM1670851v1_genomic.fna/checkm_result
[2023-06-30 14:49:55,618] [INFO] Task succeeded: CheckM
[2023-06-30 14:49:55,619] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 14:49:55,642] [INFO] ===== Completeness check finished =====
[2023-06-30 14:49:55,642] [INFO] ===== Start GTDB Search =====
[2023-06-30 14:49:55,643] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_016708515.1_ASM1670851v1_genomic.fna/markers.fasta)
[2023-06-30 14:49:55,643] [INFO] Task started: Blastn
[2023-06-30 14:49:55,643] [INFO] Running command: blastn -query GCA_016708515.1_ASM1670851v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg01fa54a5-dc44-4586-80de-01106adbe320/dqc_reference/reference_markers_gtdb.fasta -out GCA_016708515.1_ASM1670851v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 14:49:56,407] [INFO] Task succeeded: Blastn
[2023-06-30 14:49:56,413] [INFO] Selected 28 target genomes.
[2023-06-30 14:49:56,413] [INFO] Target genome list was writen to GCA_016708515.1_ASM1670851v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 14:49:56,453] [INFO] Task started: fastANI
[2023-06-30 14:49:56,453] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ea29a96-050c-482e-82dc-ad4d3e43aa2f/GCA_016708515.1_ASM1670851v1_genomic.fna.gz --refList GCA_016708515.1_ASM1670851v1_genomic.fna/target_genomes_gtdb.txt --output GCA_016708515.1_ASM1670851v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 14:50:14,000] [INFO] Task succeeded: fastANI
[2023-06-30 14:50:14,008] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 14:50:14,008] [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_016707785.1	s__UBA4417 sp016707785	97.1272	1391	1590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	97.10	97.10	0.88	0.88	2	conclusive
GCA_016707705.1	s__UBA4417 sp016707705	80.4003	269	1590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_013376995.1	s__UBA4417 sp013376995	76.8681	212	1590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903879715.1	s__UBA4417 sp903879715	76.4981	92	1590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.96	99.96	0.96	0.96	2	-
GCA_903887815.1	s__UBA4417 sp903887815	76.4234	51	1590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__UBA4417;g__UBA4417	95.0	99.90	99.90	0.90	0.90	2	-
GCA_009773455.1	s__Lentimicrobium sp009773455	75.766	54	1590	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Bacteroidales;f__Lentimicrobiaceae;g__Lentimicrobium	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 14:50:14,010] [INFO] GTDB search result was written to GCA_016708515.1_ASM1670851v1_genomic.fna/result_gtdb.tsv
[2023-06-30 14:50:14,011] [INFO] ===== GTDB Search completed =====
[2023-06-30 14:50:14,014] [INFO] DFAST_QC result json was written to GCA_016708515.1_ASM1670851v1_genomic.fna/dqc_result.json
[2023-06-30 14:50:14,014] [INFO] DFAST_QC completed!
[2023-06-30 14:50:14,014] [INFO] Total running time: 0h1m60s