[2024-01-24 14:39:15,022] [INFO] DFAST_QC pipeline started.
[2024-01-24 14:39:15,024] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 14:39:15,024] [INFO] DQC Reference Directory: /var/lib/cwl/stgbd06d1e8-3a3e-4084-b073-2fd16cb8089c/dqc_reference
[2024-01-24 14:39:16,412] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 14:39:16,413] [INFO] Task started: Prodigal
[2024-01-24 14:39:16,413] [INFO] Running command: gunzip -c /var/lib/cwl/stg3a918661-1f6b-4dc0-9f2a-d56be4bf901e/GCF_006543045.1_ASM654304v1_genomic.fna.gz | prodigal -d GCF_006543045.1_ASM654304v1_genomic.fna/cds.fna -a GCF_006543045.1_ASM654304v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 14:39:38,829] [INFO] Task succeeded: Prodigal
[2024-01-24 14:39:38,829] [INFO] Task started: HMMsearch
[2024-01-24 14:39:38,829] [INFO] Running command: hmmsearch --tblout GCF_006543045.1_ASM654304v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stgbd06d1e8-3a3e-4084-b073-2fd16cb8089c/dqc_reference/reference_markers.hmm GCF_006543045.1_ASM654304v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 14:39:39,080] [INFO] Task succeeded: HMMsearch
[2024-01-24 14:39:39,082] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg3a918661-1f6b-4dc0-9f2a-d56be4bf901e/GCF_006543045.1_ASM654304v1_genomic.fna.gz]
[2024-01-24 14:39:39,120] [INFO] Query marker FASTA was written to GCF_006543045.1_ASM654304v1_genomic.fna/markers.fasta
[2024-01-24 14:39:39,121] [INFO] Task started: Blastn
[2024-01-24 14:39:39,121] [INFO] Running command: blastn -query GCF_006543045.1_ASM654304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd06d1e8-3a3e-4084-b073-2fd16cb8089c/dqc_reference/reference_markers.fasta -out GCF_006543045.1_ASM654304v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:39:39,644] [INFO] Task succeeded: Blastn
[2024-01-24 14:39:39,648] [INFO] Selected 14 target genomes.
[2024-01-24 14:39:39,648] [INFO] Target genome list was writen to GCF_006543045.1_ASM654304v1_genomic.fna/target_genomes.txt
[2024-01-24 14:39:39,654] [INFO] Task started: fastANI
[2024-01-24 14:39:39,654] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a918661-1f6b-4dc0-9f2a-d56be4bf901e/GCF_006543045.1_ASM654304v1_genomic.fna.gz --refList GCF_006543045.1_ASM654304v1_genomic.fna/target_genomes.txt --output GCF_006543045.1_ASM654304v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 14:39:53,632] [INFO] Task succeeded: fastANI
[2024-01-24 14:39:53,633] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stgbd06d1e8-3a3e-4084-b073-2fd16cb8089c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 14:39:53,633] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stgbd06d1e8-3a3e-4084-b073-2fd16cb8089c/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 14:39:53,645] [INFO] Found 14 fastANI hits (0 hits with ANI > threshold)
[2024-01-24 14:39:53,645] [INFO] The taxonomy check result is classified as 'below_threshold'.
[2024-01-24 14:39:53,645] [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
Halopiger xanaduensis	strain=SH-6	GCA_000217715.1	387343	387343	type	True	80.4454	643	1469	95	below_threshold
Natronobacterium texcoconense	strain=DSM 24767	GCA_900104065.1	1095778	1095778	type	True	80.2094	688	1469	95	below_threshold
Halopiger aswanensis	strain=DSM 13151	GCA_003610195.1	148449	148449	type	True	80.1827	669	1469	95	below_threshold
Haloterrigena salifodinae	strain=ZY19	GCA_003977755.1	2675099	2675099	type	True	80.1521	647	1469	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000226975.3	229731	229731	type	True	80.1426	691	1469	95	below_threshold
Halobiforma lacisalsi	strain=AJ5	GCA_000336655.1	229731	229731	type	True	80.1324	696	1469	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	79.9674	597	1469	95	below_threshold
Natrinema salaciae	strain=DSM 25055	GCA_900110865.1	1186196	1186196	type	True	79.9515	651	1469	95	below_threshold
Halopiger salifodinae	strain=KCY07-B2	GCA_000784335.1	1202768	1202768	type	True	79.9106	603	1469	95	below_threshold
Natrialba magadii	strain=ATCC 43099	GCA_000025625.1	13769	13769	type	True	79.6683	609	1469	95	below_threshold
Natrialba magadii	strain=MS-3	GCA_000337875.1	13769	13769	type	True	79.5594	607	1469	95	below_threshold
Natrialba hulunbeirensis	strain=JCM 10989	GCA_000337575.1	123783	123783	type	True	79.5548	600	1469	95	below_threshold
Natrialba aegyptia	strain=DSM 13077	GCA_000337535.1	129789	129789	type	True	79.5546	587	1469	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	79.5043	599	1469	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 14:39:53,647] [INFO] DFAST Taxonomy check result was written to GCF_006543045.1_ASM654304v1_genomic.fna/tc_result.tsv
[2024-01-24 14:39:53,647] [INFO] ===== Taxonomy check completed =====
[2024-01-24 14:39:53,648] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 14:39:53,648] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stgbd06d1e8-3a3e-4084-b073-2fd16cb8089c/dqc_reference/checkm_data
[2024-01-24 14:39:53,649] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 14:39:53,696] [INFO] Task started: CheckM
[2024-01-24 14:39:53,696] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_006543045.1_ASM654304v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_006543045.1_ASM654304v1_genomic.fna/checkm_input GCF_006543045.1_ASM654304v1_genomic.fna/checkm_result
[2024-01-24 14:40:51,484] [INFO] Task succeeded: CheckM
[2024-01-24 14:40:51,486] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 14:40:51,503] [INFO] ===== Completeness check finished =====
[2024-01-24 14:40:51,503] [INFO] ===== Start GTDB Search =====
[2024-01-24 14:40:51,503] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_006543045.1_ASM654304v1_genomic.fna/markers.fasta)
[2024-01-24 14:40:51,504] [INFO] Task started: Blastn
[2024-01-24 14:40:51,504] [INFO] Running command: blastn -query GCF_006543045.1_ASM654304v1_genomic.fna/markers.fasta -db /var/lib/cwl/stgbd06d1e8-3a3e-4084-b073-2fd16cb8089c/dqc_reference/reference_markers_gtdb.fasta -out GCF_006543045.1_ASM654304v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 14:40:52,035] [INFO] Task succeeded: Blastn
[2024-01-24 14:40:52,038] [INFO] Selected 12 target genomes.
[2024-01-24 14:40:52,038] [INFO] Target genome list was writen to GCF_006543045.1_ASM654304v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 14:40:52,046] [INFO] Task started: fastANI
[2024-01-24 14:40:52,046] [INFO] Running command: fastANI --query /var/lib/cwl/stg3a918661-1f6b-4dc0-9f2a-d56be4bf901e/GCF_006543045.1_ASM654304v1_genomic.fna.gz --refList GCF_006543045.1_ASM654304v1_genomic.fna/target_genomes_gtdb.txt --output GCF_006543045.1_ASM654304v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 14:41:04,470] [INFO] Task succeeded: fastANI
[2024-01-24 14:41:04,480] [INFO] Found 12 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 14:41:04,481] [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_006543045.1	s__Salinadaptatus halalkaliphilus	100.0	1465	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Salinadaptatus	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_000217715.1	s__Halopiger xanaduensis	80.4632	641	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001953745.1	s__Natrinema saccharevitans	80.4247	625	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCA_000690595.2	s__Natrinema mahii	80.3869	624	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	N/A	N/A	N/A	N/A	1	-
GCF_005576615.1	s__Natrinema versiforme_A	80.3462	658	1469	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	80.2211	664	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halopiger	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900104065.1	s__Natronobacterium texcoconense	80.174	695	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000226975.2	s__Halobiforma lacisalsi	80.1565	687	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Halobiforma	95.4693	99.98	99.98	1.00	1.00	2	-
GCF_001861355.1	s__Natrialba sp001861355	80.1461	632	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900110455.1	s__Natrinema salifodinae	79.9733	596	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrinema	95.0	100.00	100.00	0.98	0.98	2	-
GCF_000025625.1	s__Natrialba magadii	79.667	608	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000337575.1	s__Natrialba hulunbeirensis	79.5805	596	1469	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 14:41:04,482] [INFO] GTDB search result was written to GCF_006543045.1_ASM654304v1_genomic.fna/result_gtdb.tsv
[2024-01-24 14:41:04,483] [INFO] ===== GTDB Search completed =====
[2024-01-24 14:41:04,486] [INFO] DFAST_QC result json was written to GCF_006543045.1_ASM654304v1_genomic.fna/dqc_result.json
[2024-01-24 14:41:04,487] [INFO] DFAST_QC completed!
[2024-01-24 14:41:04,487] [INFO] Total running time: 0h1m49s