[2024-01-24 14:54:56,150] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:54:56,153] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:54:56,153] [INFO] DQC Reference Directory: /var/lib/cwl/stg2634ce43-e48e-4d1a-adf9-0269f20a1c1b/dqc_reference
[2024-01-24 14:54:57,563] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:54:57,564] [INFO] Task started: Prodigal
[2024-01-24 14:54:57,564] [INFO] Running command: gunzip -c /var/lib/cwl/stgfa8b8407-5a21-41ad-936d-b366b2fd3ba3/GCF_003430825.1_ASM343082v1_genomic.fna.gz | prodigal -d GCF_003430825.1_ASM343082v1_genomic.fna/cds.fna -a GCF_003430825.1_ASM343082v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:55:15,994] [INFO] Task succeeded: Prodigal
[2024-01-24 14:55:15,995] [INFO] Task started: HMMsearch
[2024-01-24 14:55:15,995] [INFO] Running command: hmmsearch --tblout GCF_003430825.1_ASM343082v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg2634ce43-e48e-4d1a-adf9-0269f20a1c1b/dqc_reference/reference_markers.hmm GCF_003430825.1_ASM343082v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:55:16,299] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:55:16,301] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgfa8b8407-5a21-41ad-936d-b366b2fd3ba3/GCF_003430825.1_ASM343082v1_genomic.fna.gz]
[2024-01-24 14:55:16,336] [INFO] Query marker FASTA was written to GCF_003430825.1_ASM343082v1_genomic.fna/markers.fasta
[2024-01-24 14:55:16,336] [INFO] Task started: Blastn
[2024-01-24 14:55:16,336] [INFO] Running command: blastn -query GCF_003430825.1_ASM343082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2634ce43-e48e-4d1a-adf9-0269f20a1c1b/dqc_reference/reference_markers.fasta -out GCF_003430825.1_ASM343082v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:55:16,863] [INFO] Task succeeded: Blastn
[2024-01-24 14:55:16,866] [INFO] Selected 13 target genomes.
[2024-01-24 14:55:16,867] [INFO] Target genome list was writen to GCF_003430825.1_ASM343082v1_genomic.fna/target_genomes.txt
[2024-01-24 14:55:16,872] [INFO] Task started: fastANI
[2024-01-24 14:55:16,873] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8b8407-5a21-41ad-936d-b366b2fd3ba3/GCF_003430825.1_ASM343082v1_genomic.fna.gz --refList GCF_003430825.1_ASM343082v1_genomic.fna/target_genomes.txt --output GCF_003430825.1_ASM343082v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:55:29,466] [INFO] Task succeeded: fastANI
[2024-01-24 14:55:29,466] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg2634ce43-e48e-4d1a-adf9-0269f20a1c1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:55:29,467] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg2634ce43-e48e-4d1a-adf9-0269f20a1c1b/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:55:29,478] [INFO] Found 13 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:55:29,478] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:55:29,479] [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
Natronobacterium texcoconense	strain=DSM 24767	GCA_900104065.1	1095778	1095778	type	True	80.2301	689	1261	95	below_threshold
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	80.0194	624	1261	95	below_threshold
Halobiforma haloterrestris	strain=DSM 13078	GCA_900112205.1	148448	148448	type	True	79.9878	680	1261	95	below_threshold
Natronorubrum sulfidifaciens	strain=JCM 14089	GCA_000337735.1	388259	388259	type	True	79.9812	596	1261	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	79.9753	676	1261	95	below_threshold
Haloterrigena salina	strain=JCM 13891	GCA_000337495.1	504937	504937	type	True	79.9371	634	1261	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	79.8787	641	1261	95	below_threshold
Natrinema altunense	strain=AJ2	GCA_000731985.1	222984	222984	type	True	79.8072	561	1261	95	below_threshold
Natrinema altunense	strain=JCM 12890	GCA_000337155.1	222984	222984	type	True	79.7872	556	1261	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	79.7257	610	1261	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.6915	615	1261	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.6701	592	1261	95	below_threshold
Natrinema pallidum	strain=DSM 3751	GCA_000337615.1	69527	69527	type	True	79.6338	529	1261	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:55:29,480] [INFO] DFAST Taxonomy check result was written to GCF_003430825.1_ASM343082v1_genomic.fna/tc_result.tsv
[2024-01-24 14:55:29,481] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:55:29,481] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:55:29,481] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg2634ce43-e48e-4d1a-adf9-0269f20a1c1b/dqc_reference/checkm_data
[2024-01-24 14:55:29,482] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:55:29,530] [INFO] Task started: CheckM
[2024-01-24 14:55:29,530] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_003430825.1_ASM343082v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_003430825.1_ASM343082v1_genomic.fna/checkm_input GCF_003430825.1_ASM343082v1_genomic.fna/checkm_result
[2024-01-24 14:56:22,858] [INFO] Task succeeded: CheckM
[2024-01-24 14:56:22,860] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:56:22,889] [INFO] ===== Completeness check finished =====
[2024-01-24 14:56:22,890] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:56:22,890] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_003430825.1_ASM343082v1_genomic.fna/markers.fasta)
[2024-01-24 14:56:22,891] [INFO] Task started: Blastn
[2024-01-24 14:56:22,891] [INFO] Running command: blastn -query GCF_003430825.1_ASM343082v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg2634ce43-e48e-4d1a-adf9-0269f20a1c1b/dqc_reference/reference_markers_gtdb.fasta -out GCF_003430825.1_ASM343082v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:56:23,418] [INFO] Task succeeded: Blastn
[2024-01-24 14:56:23,422] [INFO] Selected 10 target genomes.
[2024-01-24 14:56:23,422] [INFO] Target genome list was writen to GCF_003430825.1_ASM343082v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:56:23,431] [INFO] Task started: fastANI
[2024-01-24 14:56:23,432] [INFO] Running command: fastANI --query /var/lib/cwl/stgfa8b8407-5a21-41ad-936d-b366b2fd3ba3/GCF_003430825.1_ASM343082v1_genomic.fna.gz --refList GCF_003430825.1_ASM343082v1_genomic.fna/target_genomes_gtdb.txt --output GCF_003430825.1_ASM343082v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:56:32,970] [INFO] Task succeeded: fastANI
[2024-01-24 14:56:32,982] [INFO] Found 10 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:56:32,982] [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_003430825.1	s__Natrarchaeobaculum sulfurireducens	100.0	1261	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	99.22	99.22	0.92	0.92	2	conclusive
GCA_001563805.1	s__Natrarchaeobaculum sp001563805	88.4821	691	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_002156705.1	s__Natrarchaeobaculum aegyptiacum	81.0839	747	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobaculum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337215.1	s__Natronolimnohabitans innermongolicus	80.3861	685	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronolimnohabitans	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025325.1	s__Haloterrigena turkmenica	79.9903	645	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	79.9837	675	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_000731985.1	s__Natrinema altunense	79.8697	554	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.98	98.00	0.96	0.93	4	-
GCF_003977755.1	s__Haloterrigena salifodinae	79.7433	608	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Haloterrigena	95.0	98.23	98.23	0.92	0.92	2	-
GCF_008245225.1	s__Natrarchaeobius swarupiae	79.7233	624	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrarchaeobius	95.0	96.49	96.49	0.86	0.86	2	-
GCF_000337615.1	s__Natrinema pallidum	79.6372	529	1261	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	98.94	98.94	0.86	0.86	2	-
--------------------------------------------------------------------------------
[2024-01-24 14:56:32,984] [INFO] GTDB search result was written to GCF_003430825.1_ASM343082v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:56:32,985] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:56:32,988] [INFO] DFAST_QC result json was written to GCF_003430825.1_ASM343082v1_genomic.fna/dqc_result.json
[2024-01-24 14:56:32,988] [INFO] DFAST_QC completed!
[2024-01-24 14:56:32,988] [INFO] Total running time: 0h1m37s