[2023-06-26 20:47:38,090] [INFO] DFAST_QC pipeline started.
[2023-06-26 20:47:38,093] [INFO] DFAST_QC version: 0.5.7
[2023-06-26 20:47:38,093] [INFO] DQC Reference Directory: /var/lib/cwl/stg9b26ae25-5486-4d38-9abc-b7e7ea741336/dqc_reference
[2023-06-26 20:47:39,606] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-26 20:47:39,607] [INFO] Task started: Prodigal
[2023-06-26 20:47:39,607] [INFO] Running command: gunzip -c /var/lib/cwl/stg797b6156-614c-4460-bbf9-d57ef2201a84/GCA_026988975.1_ASM2698897v1_genomic.fna.gz | prodigal -d GCA_026988975.1_ASM2698897v1_genomic.fna/cds.fna -a GCA_026988975.1_ASM2698897v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-26 20:47:43,288] [INFO] Task succeeded: Prodigal
[2023-06-26 20:47:43,288] [INFO] Task started: HMMsearch
[2023-06-26 20:47:43,288] [INFO] Running command: hmmsearch --tblout GCA_026988975.1_ASM2698897v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9b26ae25-5486-4d38-9abc-b7e7ea741336/dqc_reference/reference_markers.hmm GCA_026988975.1_ASM2698897v1_genomic.fna/protein.faa > /dev/null
[2023-06-26 20:47:43,467] [INFO] Task succeeded: HMMsearch
[2023-06-26 20:47:43,468] [INFO] Found 6/6 markers.
[2023-06-26 20:47:43,489] [INFO] Query marker FASTA was written to GCA_026988975.1_ASM2698897v1_genomic.fna/markers.fasta
[2023-06-26 20:47:43,490] [INFO] Task started: Blastn
[2023-06-26 20:47:43,490] [INFO] Running command: blastn -query GCA_026988975.1_ASM2698897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b26ae25-5486-4d38-9abc-b7e7ea741336/dqc_reference/reference_markers.fasta -out GCA_026988975.1_ASM2698897v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 20:47:44,009] [INFO] Task succeeded: Blastn
[2023-06-26 20:47:44,011] [INFO] Selected 29 target genomes.
[2023-06-26 20:47:44,012] [INFO] Target genome list was writen to GCA_026988975.1_ASM2698897v1_genomic.fna/target_genomes.txt
[2023-06-26 20:47:44,074] [INFO] Task started: fastANI
[2023-06-26 20:47:44,075] [INFO] Running command: fastANI --query /var/lib/cwl/stg797b6156-614c-4460-bbf9-d57ef2201a84/GCA_026988975.1_ASM2698897v1_genomic.fna.gz --refList GCA_026988975.1_ASM2698897v1_genomic.fna/target_genomes.txt --output GCA_026988975.1_ASM2698897v1_genomic.fna/fastani_result.tsv --threads 1
[2023-06-26 20:47:53,444] [INFO] Task succeeded: fastANI
[2023-06-26 20:47:53,445] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9b26ae25-5486-4d38-9abc-b7e7ea741336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-26 20:47:53,445] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9b26ae25-5486-4d38-9abc-b7e7ea741336/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-26 20:47:53,448] [INFO] Found 1 fastANI hits (0 hits with ANI > threshold)
[2023-06-26 20:47:53,448] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2023-06-26 20:47:53,449] [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
Sulfurospirillum arcachonense	strain=DSM 9755	GCA_000597725.1	57666	57666	type	True	76.4667	101	632	95	below_threshold
--------------------------------------------------------------------------------
[2023-06-26 20:47:53,450] [INFO] DFAST Taxonomy check result was written to GCA_026988975.1_ASM2698897v1_genomic.fna/tc_result.tsv
[2023-06-26 20:47:53,450] [INFO] ===== Taxonomy check completed =====
[2023-06-26 20:47:53,451] [INFO] ===== Start completeness check using CheckM =====
[2023-06-26 20:47:53,451] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9b26ae25-5486-4d38-9abc-b7e7ea741336/dqc_reference/checkm_data
[2023-06-26 20:47:53,451] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-26 20:47:53,477] [INFO] Task started: CheckM
[2023-06-26 20:47:53,477] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_026988975.1_ASM2698897v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_026988975.1_ASM2698897v1_genomic.fna/checkm_input GCA_026988975.1_ASM2698897v1_genomic.fna/checkm_result
[2023-06-26 20:48:10,029] [INFO] Task succeeded: CheckM
[2023-06-26 20:48:10,029] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-26 20:48:10,044] [INFO] ===== Completeness check finished =====
[2023-06-26 20:48:10,044] [INFO] ===== Start GTDB Search =====
[2023-06-26 20:48:10,044] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_026988975.1_ASM2698897v1_genomic.fna/markers.fasta)
[2023-06-26 20:48:10,044] [INFO] Task started: Blastn
[2023-06-26 20:48:10,044] [INFO] Running command: blastn -query GCA_026988975.1_ASM2698897v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9b26ae25-5486-4d38-9abc-b7e7ea741336/dqc_reference/reference_markers_gtdb.fasta -out GCA_026988975.1_ASM2698897v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-26 20:48:10,736] [INFO] Task succeeded: Blastn
[2023-06-26 20:48:10,739] [INFO] Selected 29 target genomes.
[2023-06-26 20:48:10,739] [INFO] Target genome list was writen to GCA_026988975.1_ASM2698897v1_genomic.fna/target_genomes_gtdb.txt
[2023-06-26 20:48:10,752] [INFO] Task started: fastANI
[2023-06-26 20:48:10,752] [INFO] Running command: fastANI --query /var/lib/cwl/stg797b6156-614c-4460-bbf9-d57ef2201a84/GCA_026988975.1_ASM2698897v1_genomic.fna.gz --refList GCA_026988975.1_ASM2698897v1_genomic.fna/target_genomes_gtdb.txt --output GCA_026988975.1_ASM2698897v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-26 20:48:21,235] [INFO] Task succeeded: fastANI
[2023-06-26 20:48:21,238] [INFO] Found 3 fastANI hits (0 hits with ANI > circumscription radius)
[2023-06-26 20:48:21,239] [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_013151055.1	s__JAADIZ01 sp013151055	78.5046	245	632	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__JAADIZ01	95.0	N/A	N/A	N/A	N/A	1	-
GCA_016735235.1	s__Sulfurospirillum_A sp016735235	76.5136	57	632	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	99.48	99.48	0.88	0.88	2	-
GCF_000597725.1	s__Sulfurospirillum_A arcachonense	76.4667	101	632	d__Bacteria;p__Campylobacterota;c__Campylobacteria;o__Campylobacterales;f__Sulfurospirillaceae;g__Sulfurospirillum_A	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-26 20:48:21,240] [INFO] GTDB search result was written to GCA_026988975.1_ASM2698897v1_genomic.fna/result_gtdb.tsv
[2023-06-26 20:48:21,240] [INFO] ===== GTDB Search completed =====
[2023-06-26 20:48:21,242] [INFO] DFAST_QC result json was written to GCA_026988975.1_ASM2698897v1_genomic.fna/dqc_result.json
[2023-06-26 20:48:21,243] [INFO] DFAST_QC completed!
[2023-06-26 20:48:21,243] [INFO] Total running time: 0h0m43s