[2024-01-25 19:53:05,597] [INFO] DFAST_QC pipeline started.
[2024-01-25 19:53:05,598] [INFO] DFAST_QC version: 0.5.7
[2024-01-25 19:53:05,598] [INFO] DQC Reference Directory: /var/lib/cwl/stgbe448a2b-0e7c-41b7-a829-a5d16722b8d6/dqc_reference
[2024-01-25 19:53:06,837] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-25 19:53:06,838] [INFO] Task started: Prodigal
[2024-01-25 19:53:06,838] [INFO] Running command: gunzip -c /var/lib/cwl/stg288395ac-eaf8-47c8-8c19-2a5cd6c09e92/GCF_017357105.1_ASM1735710v2_genomic.fna.gz | prodigal -d GCF_017357105.1_ASM1735710v2_genomic.fna/cds.fna -a GCF_017357105.1_ASM1735710v2_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-25 19:53:23,822] [INFO] Task succeeded: Prodigal
[2024-01-25 19:53:23,822] [INFO] Task started: HMMsearch
[2024-01-25 19:53:23,822] [INFO] Running command: hmmsearch --tblout GCF_017357105.1_ASM1735710v2_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbe448a2b-0e7c-41b7-a829-a5d16722b8d6/dqc_reference/reference_markers.hmm GCF_017357105.1_ASM1735710v2_genomic.fna/protein.faa > /dev/null
[2024-01-25 19:53:24,019] [INFO] Task succeeded: HMMsearch
[2024-01-25 19:53:24,020] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg288395ac-eaf8-47c8-8c19-2a5cd6c09e92/GCF_017357105.1_ASM1735710v2_genomic.fna.gz]
[2024-01-25 19:53:24,051] [INFO] Query marker FASTA was written to GCF_017357105.1_ASM1735710v2_genomic.fna/markers.fasta
[2024-01-25 19:53:24,051] [INFO] Task started: Blastn
[2024-01-25 19:53:24,051] [INFO] Running command: blastn -query GCF_017357105.1_ASM1735710v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe448a2b-0e7c-41b7-a829-a5d16722b8d6/dqc_reference/reference_markers.fasta -out GCF_017357105.1_ASM1735710v2_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:53:24,540] [INFO] Task succeeded: Blastn
[2024-01-25 19:53:24,543] [INFO] Selected 12 target genomes.
[2024-01-25 19:53:24,543] [INFO] Target genome list was writen to GCF_017357105.1_ASM1735710v2_genomic.fna/target_genomes.txt
[2024-01-25 19:53:24,551] [INFO] Task started: fastANI
[2024-01-25 19:53:24,551] [INFO] Running command: fastANI --query /var/lib/cwl/stg288395ac-eaf8-47c8-8c19-2a5cd6c09e92/GCF_017357105.1_ASM1735710v2_genomic.fna.gz --refList GCF_017357105.1_ASM1735710v2_genomic.fna/target_genomes.txt --output GCF_017357105.1_ASM1735710v2_genomic.fna/fastani_result.tsv --threads 1
[2024-01-25 19:53:34,814] [INFO] Task succeeded: fastANI
[2024-01-25 19:53:34,814] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbe448a2b-0e7c-41b7-a829-a5d16722b8d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-25 19:53:34,815] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbe448a2b-0e7c-41b7-a829-a5d16722b8d6/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-25 19:53:34,824] [INFO] Found 12 fastANI hits (0 hits with ANI > threshold)
[2024-01-25 19:53:34,824] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-25 19:53:34,824] [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 jeotgali	strain=DSM 18795	GCA_000337695.1	413812	413812	type	True	79.6301	556	1410	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.4815	548	1410	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.473	552	1410	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	79.3274	609	1410	95	below_threshold
Natronococcus amylolyticus	strain=DSM 10524	GCA_000337675.1	44470	44470	type	True	79.133	591	1410	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.125	563	1410	95	below_threshold
Natrinema versiforme	strain=JCM 10478	GCA_000337195.1	88724	88724	type	True	79.0317	550	1410	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	79.0313	596	1410	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	78.8371	505	1410	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	78.8356	515	1410	95	below_threshold
Haloterrigena hispanica	strain=DSM 18328	GCA_004217335.1	392421	392421	type	True	78.798	468	1410	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	78.6922	507	1410	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-25 19:53:34,825] [INFO] DFAST Taxonomy check result was written to GCF_017357105.1_ASM1735710v2_genomic.fna/tc_result.tsv
[2024-01-25 19:53:34,826] [INFO] ===== Taxonomy check completed =====
[2024-01-25 19:53:34,826] [INFO] ===== Start completeness check using CheckM =====
[2024-01-25 19:53:34,826] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbe448a2b-0e7c-41b7-a829-a5d16722b8d6/dqc_reference/checkm_data
[2024-01-25 19:53:34,827] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-25 19:53:34,876] [INFO] Task started: CheckM
[2024-01-25 19:53:34,879] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_017357105.1_ASM1735710v2_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_017357105.1_ASM1735710v2_genomic.fna/checkm_input GCF_017357105.1_ASM1735710v2_genomic.fna/checkm_result
[2024-01-25 19:54:21,560] [INFO] Task succeeded: CheckM
[2024-01-25 19:54:21,561] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-25 19:54:21,584] [INFO] ===== Completeness check finished =====
[2024-01-25 19:54:21,584] [INFO] ===== Start GTDB Search =====
[2024-01-25 19:54:21,585] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_017357105.1_ASM1735710v2_genomic.fna/markers.fasta)
[2024-01-25 19:54:21,585] [INFO] Task started: Blastn
[2024-01-25 19:54:21,585] [INFO] Running command: blastn -query GCF_017357105.1_ASM1735710v2_genomic.fna/markers.fasta -db /var/lib/cwl/stgbe448a2b-0e7c-41b7-a829-a5d16722b8d6/dqc_reference/reference_markers_gtdb.fasta -out GCF_017357105.1_ASM1735710v2_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-25 19:54:22,144] [INFO] Task succeeded: Blastn
[2024-01-25 19:54:22,148] [INFO] Selected 12 target genomes.
[2024-01-25 19:54:22,148] [INFO] Target genome list was writen to GCF_017357105.1_ASM1735710v2_genomic.fna/target_genomes_gtdb.txt
[2024-01-25 19:54:22,157] [INFO] Task started: fastANI
[2024-01-25 19:54:22,157] [INFO] Running command: fastANI --query /var/lib/cwl/stg288395ac-eaf8-47c8-8c19-2a5cd6c09e92/GCF_017357105.1_ASM1735710v2_genomic.fna.gz --refList GCF_017357105.1_ASM1735710v2_genomic.fna/target_genomes_gtdb.txt --output GCF_017357105.1_ASM1735710v2_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-25 19:54:32,867] [INFO] Task succeeded: fastANI
[2024-01-25 19:54:32,875] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-25 19:54:32,875] [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_017357105.1	s__Tc-Br11 sp017357105	100.0	1334	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000337695.1	s__Natronococcus jeotgali	79.5932	561	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	95.54	95.54	0.86	0.86	2	-
GCA_001564275.1	s__Tc-Br11 sp001564275	79.5832	506	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Tc-Br11	95.0	99.79	99.79	0.91	0.91	2	-
GCF_900110455.1	s__Natrinema salifodinae	79.4817	552	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCA_000690595.2	s__Natrinema mahii	79.457	546	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003610195.1	s__Halopiger aswanensis	79.3686	604	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_013456555.1	s__Natrinema sp013456555	79.1938	536	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337675.1	s__Natronococcus amylolyticus	79.1607	588	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCA_003559215.1	s__Natronococcus sp003559215	79.1273	539	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	99.83	99.81	0.98	0.98	4	-
GCF_000337195.1	s__Natrinema versiforme	79.0693	545	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110865.1	s__Natrinema salaciae	79.0505	592	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000731985.1	s__Natrinema altunense	78.8438	515	1410	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	-
--------------------------------------------------------------------------------
[2024-01-25 19:54:32,877] [INFO] GTDB search result was written to GCF_017357105.1_ASM1735710v2_genomic.fna/result_gtdb.tsv
[2024-01-25 19:54:32,877] [INFO] ===== GTDB Search completed =====
[2024-01-25 19:54:32,880] [INFO] DFAST_QC result json was written to GCF_017357105.1_ASM1735710v2_genomic.fna/dqc_result.json
[2024-01-25 19:54:32,880] [INFO] DFAST_QC completed!
[2024-01-25 19:54:32,880] [INFO] Total running time: 0h1m27s