[2023-06-28 15:41:47,825] [INFO] DFAST_QC pipeline started.
[2023-06-28 15:41:47,827] [INFO] DFAST_QC version: 0.5.7
[2023-06-28 15:41:47,827] [INFO] DQC Reference Directory: /var/lib/cwl/stg395959d6-0384-454c-9dcd-b4f93cca10d6/dqc_reference
[2023-06-28 15:41:48,940] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-28 15:41:48,940] [INFO] Task started: Prodigal
[2023-06-28 15:41:48,941] [INFO] Running command: gunzip -c /var/lib/cwl/stg9c16f1c1-805b-4d54-92bd-f1aec6192baf/GCA_020161355.1_ASM2016135v1_genomic.fna.gz | prodigal -d GCA_020161355.1_ASM2016135v1_genomic.fna/cds.fna -a GCA_020161355.1_ASM2016135v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-28 15:42:06,056] [INFO] Task succeeded: Prodigal
[2023-06-28 15:42:06,056] [INFO] Task started: HMMsearch
[2023-06-28 15:42:06,057] [INFO] Running command: hmmsearch --tblout GCA_020161355.1_ASM2016135v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg395959d6-0384-454c-9dcd-b4f93cca10d6/dqc_reference/reference_markers.hmm GCA_020161355.1_ASM2016135v1_genomic.fna/protein.faa > /dev/null
[2023-06-28 15:42:06,285] [INFO] Task succeeded: HMMsearch
[2023-06-28 15:42:06,287] [INFO] Found 6/6 markers.
[2023-06-28 15:42:06,319] [INFO] Query marker FASTA was written to GCA_020161355.1_ASM2016135v1_genomic.fna/markers.fasta
[2023-06-28 15:42:06,319] [INFO] Task started: Blastn
[2023-06-28 15:42:06,319] [INFO] Running command: blastn -query GCA_020161355.1_ASM2016135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg395959d6-0384-454c-9dcd-b4f93cca10d6/dqc_reference/reference_markers.fasta -out GCA_020161355.1_ASM2016135v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:42:06,858] [INFO] Task succeeded: Blastn
[2023-06-28 15:42:06,862] [INFO] Selected 24 target genomes.
[2023-06-28 15:42:06,862] [INFO] Target genome list was writen to GCA_020161355.1_ASM2016135v1_genomic.fna/target_genomes.txt
[2023-06-28 15:42:06,903] [INFO] Task started: fastANI
[2023-06-28 15:42:06,903] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c16f1c1-805b-4d54-92bd-f1aec6192baf/GCA_020161355.1_ASM2016135v1_genomic.fna.gz --refList GCA_020161355.1_ASM2016135v1_genomic.fna/target_genomes.txt --output GCA_020161355.1_ASM2016135v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-28 15:42:24,378] [INFO] Task succeeded: fastANI
[2023-06-28 15:42:24,378] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg395959d6-0384-454c-9dcd-b4f93cca10d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-28 15:42:24,379] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg395959d6-0384-454c-9dcd-b4f93cca10d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-28 15:42:24,385] [INFO] Found 5 fastANI hits (0 hits with ANI > threshold)
[2023-06-28 15:42:24,385] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-28 15:42:24,385] [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
Lacihabitans soyangensis	strain=KCTC23259	GCA_024343775.1	869394	869394	type	True	78.3934	235	1596	95	below_threshold
Leadbetterella byssophila	strain=DSM 17132	GCA_000166395.1	316068	316068	type	True	76.6453	62	1596	95	below_threshold
Jiulongibacter sediminis	strain=JN14-9	GCA_004329705.1	1605367	1605367	type	True	75.5495	67	1596	95	below_threshold
Jiulongibacter sediminis	strain=JN14-9	GCA_001306455.1	1605367	1605367	type	True	75.5494	67	1596	95	below_threshold
Emticicia agri	strain=17J42-9	GCA_004168285.1	2492393	2492393	type	True	75.4783	51	1596	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-28 15:42:24,387] [INFO] DFAST Taxonomy check result was written to GCA_020161355.1_ASM2016135v1_genomic.fna/tc_result.tsv
[2023-06-28 15:42:24,387] [INFO] ===== Taxonomy check completed =====
[2023-06-28 15:42:24,387] [INFO] ===== Start completeness check using CheckM =====
[2023-06-28 15:42:24,387] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg395959d6-0384-454c-9dcd-b4f93cca10d6/dqc_reference/checkm_data
[2023-06-28 15:42:24,388] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-28 15:42:24,435] [INFO] Task started: CheckM
[2023-06-28 15:42:24,435] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_020161355.1_ASM2016135v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_020161355.1_ASM2016135v1_genomic.fna/checkm_input GCA_020161355.1_ASM2016135v1_genomic.fna/checkm_result
[2023-06-28 15:43:14,538] [INFO] Task succeeded: CheckM
[2023-06-28 15:43:14,539] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 100.00%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-28 15:43:14,574] [INFO] ===== Completeness check finished =====
[2023-06-28 15:43:14,574] [INFO] ===== Start GTDB Search =====
[2023-06-28 15:43:14,575] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_020161355.1_ASM2016135v1_genomic.fna/markers.fasta)
[2023-06-28 15:43:14,575] [INFO] Task started: Blastn
[2023-06-28 15:43:14,575] [INFO] Running command: blastn -query GCA_020161355.1_ASM2016135v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg395959d6-0384-454c-9dcd-b4f93cca10d6/dqc_reference/reference_markers_gtdb.fasta -out GCA_020161355.1_ASM2016135v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-28 15:43:15,361] [INFO] Task succeeded: Blastn
[2023-06-28 15:43:15,365] [INFO] Selected 31 target genomes.
[2023-06-28 15:43:15,365] [INFO] Target genome list was writen to GCA_020161355.1_ASM2016135v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-28 15:43:15,383] [INFO] Task started: fastANI
[2023-06-28 15:43:15,383] [INFO] Running command: fastANI --query /var/lib/cwl/stg9c16f1c1-805b-4d54-92bd-f1aec6192baf/GCA_020161355.1_ASM2016135v1_genomic.fna.gz --refList GCA_020161355.1_ASM2016135v1_genomic.fna/target_genomes_gtdb.txt --output GCA_020161355.1_ASM2016135v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-28 15:43:38,520] [INFO] Task succeeded: fastANI
[2023-06-28 15:43:38,526] [INFO] Found 7 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-28 15:43:38,526] [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_016722655.1	s__Leadbetterella sp016722655	84.4343	1157	1596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	99.38	99.07	0.96	0.94	5	-
GCA_002256295.1	s__Leadbetterella sp002256295	77.2807	185	1596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	97.02	97.02	0.83	0.83	2	-
GCF_000166395.1	s__Leadbetterella byssophila	76.6119	63	1596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009905725.1	s__Leadbetterella sp002483125	76.485	107	1596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Leadbetterella	95.0	98.11	98.11	0.94	0.94	2	-
GCA_017495105.1	s__Emticicia sp017495105	75.915	53	1596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_004168285.1	s__Emticicia sp004168285	75.4783	51	1596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013912375.1	s__Emticicia sp013912375	75.2953	63	1596	d__Bacteria;p__Bacteroidota;c__Bacteroidia;o__Cytophagales;f__Spirosomaceae;g__Emticicia	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-28 15:43:38,528] [INFO] GTDB search result was written to GCA_020161355.1_ASM2016135v1_genomic.fna/result_gtdb.tsv
[2023-06-28 15:43:38,529] [INFO] ===== GTDB Search completed =====
[2023-06-28 15:43:38,531] [INFO] DFAST_QC result json was written to GCA_020161355.1_ASM2016135v1_genomic.fna/dqc_result.json
[2023-06-28 15:43:38,531] [INFO] DFAST_QC completed!
[2023-06-28 15:43:38,531] [INFO] Total running time: 0h1m51s