[2024-01-25 17:51:20,764] [INFO] DFAST_QC pipeline started.
[2024-01-25 17:51:20,765] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 17:51:20,765] [INFO] DQC Reference Directory: /var/lib/cwl/stg1d694243-15aa-4423-a7f2-30c00960e8fa/dqc_reference
[2024-01-25 17:51:21,942] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 17:51:21,943] [INFO] Task started: Prodigal
[2024-01-25 17:51:21,943] [INFO] Running command: gunzip -c /var/lib/cwl/stg09d67068-e452-4393-b13d-3e1232f1e7aa/GCF_000337675.1_ASM33767v1_genomic.fna.gz | prodigal -d GCF_000337675.1_ASM33767v1_genomic.fna/cds.fna -a GCF_000337675.1_ASM33767v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 17:51:38,322] [INFO] Task succeeded: Prodigal
[2024-01-25 17:51:38,322] [INFO] Task started: HMMsearch
[2024-01-25 17:51:38,322] [INFO] Running command: hmmsearch --tblout GCF_000337675.1_ASM33767v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg1d694243-15aa-4423-a7f2-30c00960e8fa/dqc_reference/reference_markers.hmm GCF_000337675.1_ASM33767v1_genomic.fna/protein.faa > /dev/null
[2024-01-25 17:51:38,549] [INFO] Task succeeded: HMMsearch
[2024-01-25 17:51:38,550] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg09d67068-e452-4393-b13d-3e1232f1e7aa/GCF_000337675.1_ASM33767v1_genomic.fna.gz]
[2024-01-25 17:51:38,588] [INFO] Query marker FASTA was written to GCF_000337675.1_ASM33767v1_genomic.fna/markers.fasta
[2024-01-25 17:51:38,588] [INFO] Task started: Blastn
[2024-01-25 17:51:38,588] [INFO] Running command: blastn -query GCF_000337675.1_ASM33767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d694243-15aa-4423-a7f2-30c00960e8fa/dqc_reference/reference_markers.fasta -out GCF_000337675.1_ASM33767v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:51:39,084] [INFO] Task succeeded: Blastn
[2024-01-25 17:51:39,087] [INFO] Selected 7 target genomes.
[2024-01-25 17:51:39,087] [INFO] Target genome list was writen to GCF_000337675.1_ASM33767v1_genomic.fna/target_genomes.txt
[2024-01-25 17:51:39,091] [INFO] Task started: fastANI
[2024-01-25 17:51:39,091] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d67068-e452-4393-b13d-3e1232f1e7aa/GCF_000337675.1_ASM33767v1_genomic.fna.gz --refList GCF_000337675.1_ASM33767v1_genomic.fna/target_genomes.txt --output GCF_000337675.1_ASM33767v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 17:51:47,522] [INFO] Task succeeded: fastANI
[2024-01-25 17:51:47,523] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg1d694243-15aa-4423-a7f2-30c00960e8fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 17:51:47,523] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg1d694243-15aa-4423-a7f2-30c00960e8fa/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 17:51:47,529] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-25 17:51:47,529] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-25 17:51:47,529] [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
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	100.0	1447	1450	95	conclusive
Natronococcus occultus	strain=SP4	GCA_000328685.1	29288	29288	type	True	86.9902	1091	1450	95	below_threshold
Natronococcus jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	86.5825	946	1450	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	83.0176	967	1450	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	80.9099	743	1450	95	below_threshold
Halopiger goleimassiliensis	strain=IIH3	GCA_000455345.1	1293048	1293048	type	True	80.6299	691	1450	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	80.5668	650	1450	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 17:51:47,530] [INFO] DFAST Taxonomy check result was written to GCF_000337675.1_ASM33767v1_genomic.fna/tc_result.tsv
[2024-01-25 17:51:47,530] [INFO] ===== Taxonomy check completed =====
[2024-01-25 17:51:47,531] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 17:51:47,531] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg1d694243-15aa-4423-a7f2-30c00960e8fa/dqc_reference/checkm_data
[2024-01-25 17:51:47,531] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 17:51:47,576] [INFO] Task started: CheckM
[2024-01-25 17:51:47,577] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337675.1_ASM33767v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337675.1_ASM33767v1_genomic.fna/checkm_input GCF_000337675.1_ASM33767v1_genomic.fna/checkm_result
[2024-01-25 17:52:32,297] [INFO] Task succeeded: CheckM
[2024-01-25 17:52:32,298] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 91.67%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 17:52:32,319] [INFO] ===== Completeness check finished =====
[2024-01-25 17:52:32,319] [INFO] ===== Start GTDB Search =====
[2024-01-25 17:52:32,320] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337675.1_ASM33767v1_genomic.fna/markers.fasta)
[2024-01-25 17:52:32,320] [INFO] Task started: Blastn
[2024-01-25 17:52:32,320] [INFO] Running command: blastn -query GCF_000337675.1_ASM33767v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg1d694243-15aa-4423-a7f2-30c00960e8fa/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337675.1_ASM33767v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 17:52:32,893] [INFO] Task succeeded: Blastn
[2024-01-25 17:52:32,896] [INFO] Selected 5 target genomes.
[2024-01-25 17:52:32,896] [INFO] Target genome list was writen to GCF_000337675.1_ASM33767v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 17:52:32,902] [INFO] Task started: fastANI
[2024-01-25 17:52:32,902] [INFO] Running command: fastANI --query /var/lib/cwl/stg09d67068-e452-4393-b13d-3e1232f1e7aa/GCF_000337675.1_ASM33767v1_genomic.fna.gz --refList GCF_000337675.1_ASM33767v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337675.1_ASM33767v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 17:52:39,811] [INFO] Task succeeded: fastANI
[2024-01-25 17:52:39,816] [INFO] Found 5 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 17:52:39,816] [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
GCF_000337675.1	s__Natronococcus amylolyticus	100.0	1447	1450	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCA_003559215.1	s__Natronococcus sp003559215	90.4244	1028	1450	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	99.83	99.81	0.98	0.98	4	-
GCF_000328685.1	s__Natronococcus occultus	87.0074	1089	1450	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337695.1	s__Natronococcus jeotgali	86.5283	951	1450	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCF_008122205.1	s__Natronococcus sp008122205	83.0421	964	1450	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-25 17:52:39,818] [INFO] GTDB search result was written to GCF_000337675.1_ASM33767v1_genomic.fna/result_gtdb.tsv
[2024-01-25 17:52:39,818] [INFO] ===== GTDB Search completed =====
[2024-01-25 17:52:39,820] [INFO] DFAST_QC result json was written to GCF_000337675.1_ASM33767v1_genomic.fna/dqc_result.json
[2024-01-25 17:52:39,821] [INFO] DFAST_QC completed!
[2024-01-25 17:52:39,821] [INFO] Total running time: 0h1m19s