[2024-01-24 11:35:10,467] [INFO] DFAST_QC pipeline started.
[2024-01-24 11:35:10,469] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 11:35:10,470] [INFO] DQC Reference Directory: /var/lib/cwl/stg9c39e54d-7f49-46bd-8b83-b9f21e07841a/dqc_reference
[2024-01-24 11:35:11,866] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 11:35:11,867] [INFO] Task started: Prodigal
[2024-01-24 11:35:11,867] [INFO] Running command: gunzip -c /var/lib/cwl/stga33a1ebf-450c-4865-ae0b-58c68839a0c0/GCF_017094485.1_ASM1709448v1_genomic.fna.gz | prodigal -d GCF_017094485.1_ASM1709448v1_genomic.fna/cds.fna -a GCF_017094485.1_ASM1709448v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 11:35:27,631] [INFO] Task succeeded: Prodigal
[2024-01-24 11:35:27,631] [INFO] Task started: HMMsearch
[2024-01-24 11:35:27,631] [INFO] Running command: hmmsearch --tblout GCF_017094485.1_ASM1709448v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg9c39e54d-7f49-46bd-8b83-b9f21e07841a/dqc_reference/reference_markers.hmm GCF_017094485.1_ASM1709448v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 11:35:27,877] [INFO] Task succeeded: HMMsearch
[2024-01-24 11:35:27,878] [WARNING] Found 3/6 markers. [/var/lib/cwl/stga33a1ebf-450c-4865-ae0b-58c68839a0c0/GCF_017094485.1_ASM1709448v1_genomic.fna.gz]
[2024-01-24 11:35:27,905] [INFO] Query marker FASTA was written to GCF_017094485.1_ASM1709448v1_genomic.fna/markers.fasta
[2024-01-24 11:35:27,905] [INFO] Task started: Blastn
[2024-01-24 11:35:27,905] [INFO] Running command: blastn -query GCF_017094485.1_ASM1709448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c39e54d-7f49-46bd-8b83-b9f21e07841a/dqc_reference/reference_markers.fasta -out GCF_017094485.1_ASM1709448v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:35:28,443] [INFO] Task succeeded: Blastn
[2024-01-24 11:35:28,447] [INFO] Selected 10 target genomes.
[2024-01-24 11:35:28,447] [INFO] Target genome list was writen to GCF_017094485.1_ASM1709448v1_genomic.fna/target_genomes.txt
[2024-01-24 11:35:28,452] [INFO] Task started: fastANI
[2024-01-24 11:35:28,453] [INFO] Running command: fastANI --query /var/lib/cwl/stga33a1ebf-450c-4865-ae0b-58c68839a0c0/GCF_017094485.1_ASM1709448v1_genomic.fna.gz --refList GCF_017094485.1_ASM1709448v1_genomic.fna/target_genomes.txt --output GCF_017094485.1_ASM1709448v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 11:35:36,582] [INFO] Task succeeded: fastANI
[2024-01-24 11:35:36,583] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg9c39e54d-7f49-46bd-8b83-b9f21e07841a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 11:35:36,583] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg9c39e54d-7f49-46bd-8b83-b9f21e07841a/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 11:35:36,594] [INFO] Found 10 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 11:35:36,595] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 11:35:36,595] [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
Natranaeroarchaeum sulfidigenes	strain=AArc-S	GCA_017094485.1	2784880	2784880	type	True	100.0	1013	1013	95	conclusive
Natranaeroarchaeum aerophilus	strain=AArc-St1-1	GCA_023638055.1	2917711	2917711	type	True	89.9212	808	1013	95	below_threshold
Natronoarchaeum philippinense	strain=DSM 27208	GCA_900215575.1	558529	558529	type	True	79.0921	415	1013	95	below_threshold
Natronoarchaeum rubrum	strain=GX48	GCA_024494695.1	755311	755311	type	True	79.0509	426	1013	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	77.6838	272	1013	95	below_threshold
Natrialba magadii	strain=ATCC 43099	GCA_000025625.1	13769	13769	type	True	77.5523	216	1013	95	below_threshold
Halopiger djelfimassiliensis	strain=IIH2	GCA_000455365.1	1293047	1293047	type	True	77.5508	257	1013	95	below_threshold
Natronococcus occultus	strain=SP4	GCA_000328685.1	29288	29288	type	True	77.5378	304	1013	95	below_threshold
Natronococcus pandeyae	strain=LS1_42	GCA_008122205.1	2055836	2055836	type	True	77.5022	288	1013	95	below_threshold
Natronorubrum halalkaliphilum	strain=JWXQ-INN-674	GCA_009834785.1	2691917	2691917	type	True	77.4032	257	1013	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 11:35:36,597] [INFO] DFAST Taxonomy check result was written to GCF_017094485.1_ASM1709448v1_genomic.fna/tc_result.tsv
[2024-01-24 11:35:36,597] [INFO] ===== Taxonomy check completed =====
[2024-01-24 11:35:36,597] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 11:35:36,598] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg9c39e54d-7f49-46bd-8b83-b9f21e07841a/dqc_reference/checkm_data
[2024-01-24 11:35:36,599] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 11:35:36,632] [INFO] Task started: CheckM
[2024-01-24 11:35:36,633] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017094485.1_ASM1709448v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017094485.1_ASM1709448v1_genomic.fna/checkm_input GCF_017094485.1_ASM1709448v1_genomic.fna/checkm_result
[2024-01-24 11:36:22,044] [INFO] Task succeeded: CheckM
[2024-01-24 11:36:22,046] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.55%
Strain heterogeneity: 50.00%
--------------------------------------------------------------------------------
[2024-01-24 11:36:22,068] [INFO] ===== Completeness check finished =====
[2024-01-24 11:36:22,069] [INFO] ===== Start GTDB Search =====
[2024-01-24 11:36:22,069] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017094485.1_ASM1709448v1_genomic.fna/markers.fasta)
[2024-01-24 11:36:22,070] [INFO] Task started: Blastn
[2024-01-24 11:36:22,070] [INFO] Running command: blastn -query GCF_017094485.1_ASM1709448v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg9c39e54d-7f49-46bd-8b83-b9f21e07841a/dqc_reference/reference_markers_gtdb.fasta -out GCF_017094485.1_ASM1709448v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 11:36:22,578] [INFO] Task succeeded: Blastn
[2024-01-24 11:36:22,584] [INFO] Selected 13 target genomes.
[2024-01-24 11:36:22,584] [INFO] Target genome list was writen to GCF_017094485.1_ASM1709448v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 11:36:22,608] [INFO] Task started: fastANI
[2024-01-24 11:36:22,609] [INFO] Running command: fastANI --query /var/lib/cwl/stga33a1ebf-450c-4865-ae0b-58c68839a0c0/GCF_017094485.1_ASM1709448v1_genomic.fna.gz --refList GCF_017094485.1_ASM1709448v1_genomic.fna/target_genomes_gtdb.txt --output GCF_017094485.1_ASM1709448v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 11:36:31,626] [INFO] Task succeeded: fastANI
[2024-01-24 11:36:31,645] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 11:36:31,645] [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_017094485.1	s__Natronoarchaeum sp017094485	100.0	1013	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natronoarchaeaceae;g__Natronoarchaeum	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_900215575.1	s__Natronoarchaeum philippinense	79.0978	414	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natronoarchaeaceae;g__Natronoarchaeum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002494345.1	s__Natrinema ejinorense	77.9878	262	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	95.42	95.42	0.91	0.91	2	-
GCF_000337195.1	s__Natrinema versiforme	77.6606	274	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900100335.1	s__Natronorubrum texcoconense	77.5888	282	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025625.1	s__Natrialba magadii	77.4982	216	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	99.99	99.99	1.00	1.00	2	-
GCF_008122205.1	s__Natronococcus sp008122205	77.4923	289	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000328685.1	s__Natronococcus occultus	77.4809	305	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_017357405.1	s__KZCA124 sp017357405	77.4686	269	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__KZCA124	95.0	N/A	N/A	N/A	N/A	1	-
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	77.4567	210	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_009834785.1	s__Natronorubrum halalkaliphilum	77.4032	257	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900156425.1	s__Haladaptatus litoreus	76.4037	127	1013	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haladaptataceae;g__Haladaptatus	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 11:36:31,648] [INFO] GTDB search result was written to GCF_017094485.1_ASM1709448v1_genomic.fna/result_gtdb.tsv
[2024-01-24 11:36:31,648] [INFO] ===== GTDB Search completed =====
[2024-01-24 11:36:31,652] [INFO] DFAST_QC result json was written to GCF_017094485.1_ASM1709448v1_genomic.fna/dqc_result.json
[2024-01-24 11:36:31,652] [INFO] DFAST_QC completed!
[2024-01-24 11:36:31,652] [INFO] Total running time: 0h1m21s