[2024-01-24 13:45:48,771] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:45:48,773] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:45:48,774] [INFO] DQC Reference Directory: /var/lib/cwl/stg92635ab5-275b-4dbf-a19b-193b8c9eb7c9/dqc_reference
[2024-01-24 13:45:50,195] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:45:50,196] [INFO] Task started: Prodigal
[2024-01-24 13:45:50,197] [INFO] Running command: gunzip -c /var/lib/cwl/stgaea52598-6403-4549-a929-1e6514bfef3a/GCF_000337135.1_ASM33713v1_genomic.fna.gz | prodigal -d GCF_000337135.1_ASM33713v1_genomic.fna/cds.fna -a GCF_000337135.1_ASM33713v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:46:13,331] [INFO] Task succeeded: Prodigal
[2024-01-24 13:46:13,331] [INFO] Task started: HMMsearch
[2024-01-24 13:46:13,331] [INFO] Running command: hmmsearch --tblout GCF_000337135.1_ASM33713v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg92635ab5-275b-4dbf-a19b-193b8c9eb7c9/dqc_reference/reference_markers.hmm GCF_000337135.1_ASM33713v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:46:13,626] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:46:13,628] [WARNING] Found 3/6 markers. [/var/lib/cwl/stgaea52598-6403-4549-a929-1e6514bfef3a/GCF_000337135.1_ASM33713v1_genomic.fna.gz]
[2024-01-24 13:46:13,665] [INFO] Query marker FASTA was written to GCF_000337135.1_ASM33713v1_genomic.fna/markers.fasta
[2024-01-24 13:46:13,666] [INFO] Task started: Blastn
[2024-01-24 13:46:13,666] [INFO] Running command: blastn -query GCF_000337135.1_ASM33713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92635ab5-275b-4dbf-a19b-193b8c9eb7c9/dqc_reference/reference_markers.fasta -out GCF_000337135.1_ASM33713v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:46:14,231] [INFO] Task succeeded: Blastn
[2024-01-24 13:46:14,234] [INFO] Selected 7 target genomes.
[2024-01-24 13:46:14,235] [INFO] Target genome list was writen to GCF_000337135.1_ASM33713v1_genomic.fna/target_genomes.txt
[2024-01-24 13:46:14,243] [INFO] Task started: fastANI
[2024-01-24 13:46:14,243] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea52598-6403-4549-a929-1e6514bfef3a/GCF_000337135.1_ASM33713v1_genomic.fna.gz --refList GCF_000337135.1_ASM33713v1_genomic.fna/target_genomes.txt --output GCF_000337135.1_ASM33713v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:46:22,243] [INFO] Task succeeded: fastANI
[2024-01-24 13:46:22,243] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg92635ab5-275b-4dbf-a19b-193b8c9eb7c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:46:22,244] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg92635ab5-275b-4dbf-a19b-193b8c9eb7c9/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:46:22,252] [INFO] Found 7 fastANI hits (1 hits with ANI > threshold)
[2024-01-24 13:46:22,252] [INFO] The taxonomy check result is classified as 'conclusive'.
[2024-01-24 13:46:22,252] [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
Natrialba chahannaoensis	strain=JCM 10990	GCA_000337135.1	68911	68911	type	True	100.0	1391	1394	95	conclusive
Natrialba hulunbeirensis	strain=JCM 10989	GCA_000337575.1	123783	123783	type	True	89.8152	1078	1394	95	below_threshold
Natrialba magadii	strain=MS-3	GCA_000337875.1	13769	13769	type	True	89.1638	1060	1394	95	below_threshold
Natrialba magadii	strain=ATCC 43099	GCA_000025625.1	13769	13769	type	True	89.1636	1076	1394	95	below_threshold
Natrialba aegyptia	strain=DSM 13077	GCA_000337535.1	129789	129789	type	True	81.2625	786	1394	95	below_threshold
Natrialba taiwanensis	strain=DSM 12281	GCA_000337595.1	160846	160846	type	True	81.2283	775	1394	95	below_threshold
Natrinema amylolyticum	strain=LT61	GCA_020515625.1	2878679	2878679	type	True	79.6925	599	1394	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:46:22,254] [INFO] DFAST Taxonomy check result was written to GCF_000337135.1_ASM33713v1_genomic.fna/tc_result.tsv
[2024-01-24 13:46:22,254] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:46:22,255] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:46:22,255] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg92635ab5-275b-4dbf-a19b-193b8c9eb7c9/dqc_reference/checkm_data
[2024-01-24 13:46:22,256] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:46:22,304] [INFO] Task started: CheckM
[2024-01-24 13:46:22,305] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337135.1_ASM33713v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337135.1_ASM33713v1_genomic.fna/checkm_input GCF_000337135.1_ASM33713v1_genomic.fna/checkm_result
[2024-01-24 13:47:25,407] [INFO] Task succeeded: CheckM
[2024-01-24 13:47:25,409] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:47:25,433] [INFO] ===== Completeness check finished =====
[2024-01-24 13:47:25,433] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:47:25,433] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337135.1_ASM33713v1_genomic.fna/markers.fasta)
[2024-01-24 13:47:25,434] [INFO] Task started: Blastn
[2024-01-24 13:47:25,434] [INFO] Running command: blastn -query GCF_000337135.1_ASM33713v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg92635ab5-275b-4dbf-a19b-193b8c9eb7c9/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337135.1_ASM33713v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:47:25,925] [INFO] Task succeeded: Blastn
[2024-01-24 13:47:25,929] [INFO] Selected 7 target genomes.
[2024-01-24 13:47:25,929] [INFO] Target genome list was writen to GCF_000337135.1_ASM33713v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:47:25,940] [INFO] Task started: fastANI
[2024-01-24 13:47:25,940] [INFO] Running command: fastANI --query /var/lib/cwl/stgaea52598-6403-4549-a929-1e6514bfef3a/GCF_000337135.1_ASM33713v1_genomic.fna.gz --refList GCF_000337135.1_ASM33713v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337135.1_ASM33713v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:47:33,581] [INFO] Task succeeded: fastANI
[2024-01-24 13:47:33,596] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:47:33,596] [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_000337135.1	s__Natrialba chahannaoensis	100.0	1391	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	conclusive
GCF_001861355.1	s__Natrialba sp001861355	90.0907	1105	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000337575.1	s__Natrialba hulunbeirensis	89.7793	1080	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000025625.1	s__Natrialba magadii	89.1633	1077	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	99.99	99.99	1.00	1.00	2	-
GCF_000337535.1	s__Natrialba aegyptia	81.2712	785	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.4145	N/A	N/A	N/A	N/A	1	-
GCF_000337595.1	s__Natrialba taiwanensis	81.2532	772	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.4145	N/A	N/A	N/A	N/A	1	-
GCF_900100335.1	s__Natronorubrum texcoconense	79.9306	679	1394	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronorubrum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:47:33,598] [INFO] GTDB search result was written to GCF_000337135.1_ASM33713v1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:47:33,599] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:47:33,603] [INFO] DFAST_QC result json was written to GCF_000337135.1_ASM33713v1_genomic.fna/dqc_result.json
[2024-01-24 13:47:33,603] [INFO] DFAST_QC completed!
[2024-01-24 13:47:33,603] [INFO] Total running time: 0h1m45s