[2024-01-24 12:31:21,191] [INFO] DFAST_QC pipeline started.
[2024-01-24 12:31:21,192] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 12:31:21,192] [INFO] DQC Reference Directory: /var/lib/cwl/stg4d93d2e2-438c-44ad-976c-2f1f6c508ead/dqc_reference
[2024-01-24 12:31:22,590] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 12:31:22,604] [INFO] Task started: Prodigal
[2024-01-24 12:31:22,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg4ff6d366-3dda-4453-89ad-19d461c590a7/GCF_000337595.1_ASM33759v1_genomic.fna.gz | prodigal -d GCF_000337595.1_ASM33759v1_genomic.fna/cds.fna -a GCF_000337595.1_ASM33759v1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 12:31:45,941] [INFO] Task succeeded: Prodigal
[2024-01-24 12:31:45,941] [INFO] Task started: HMMsearch
[2024-01-24 12:31:45,941] [INFO] Running command: hmmsearch --tblout GCF_000337595.1_ASM33759v1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4d93d2e2-438c-44ad-976c-2f1f6c508ead/dqc_reference/reference_markers.hmm GCF_000337595.1_ASM33759v1_genomic.fna/protein.faa > /dev/null
[2024-01-24 12:31:46,150] [INFO] Task succeeded: HMMsearch
[2024-01-24 12:31:46,152] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg4ff6d366-3dda-4453-89ad-19d461c590a7/GCF_000337595.1_ASM33759v1_genomic.fna.gz]
[2024-01-24 12:31:46,190] [INFO] Query marker FASTA was written to GCF_000337595.1_ASM33759v1_genomic.fna/markers.fasta
[2024-01-24 12:31:46,191] [INFO] Task started: Blastn
[2024-01-24 12:31:46,191] [INFO] Running command: blastn -query GCF_000337595.1_ASM33759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d93d2e2-438c-44ad-976c-2f1f6c508ead/dqc_reference/reference_markers.fasta -out GCF_000337595.1_ASM33759v1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:31:46,721] [INFO] Task succeeded: Blastn
[2024-01-24 12:31:46,725] [INFO] Selected 8 target genomes.
[2024-01-24 12:31:46,726] [INFO] Target genome list was writen to GCF_000337595.1_ASM33759v1_genomic.fna/target_genomes.txt
[2024-01-24 12:31:46,730] [INFO] Task started: fastANI
[2024-01-24 12:31:46,731] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff6d366-3dda-4453-89ad-19d461c590a7/GCF_000337595.1_ASM33759v1_genomic.fna.gz --refList GCF_000337595.1_ASM33759v1_genomic.fna/target_genomes.txt --output GCF_000337595.1_ASM33759v1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 12:31:54,794] [INFO] Task succeeded: fastANI
[2024-01-24 12:31:54,795] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4d93d2e2-438c-44ad-976c-2f1f6c508ead/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 12:31:54,795] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4d93d2e2-438c-44ad-976c-2f1f6c508ead/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 12:31:54,804] [INFO] Found 8 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 12:31:54,804] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 12:31:54,804] [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 taiwanensis	strain=DSM 12281	GCA_000337595.1	160846	160846	type	True	100.0	1509	1513	95	inconclusive
Natrialba aegyptia	strain=DSM 13077	GCA_000337535.1	129789	129789	type	True	95.4158	1292	1513	95	inconclusive
Natrialba asiatica	strain=DSM 12278	GCA_000337555.1	64602	64602	type	True	93.9443	1190	1513	95	below_threshold
Natrialba hulunbeirensis	strain=JCM 10989	GCA_000337575.1	123783	123783	type	True	81.7563	801	1513	95	below_threshold
Natrialba magadii	strain=ATCC 43099	GCA_000025625.1	13769	13769	type	True	81.6178	794	1513	95	below_threshold
Halopiger salifodinae	strain=CGMCC 1.12284	GCA_900110455.1	1202768	1202768	type	True	80.5075	733	1513	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_900114025.1	44930	44930	type	True	79.5047	539	1513	95	below_threshold
Natronobacterium gregoryi	strain=SP2	GCA_002855455.1	44930	44930	type	True	79.4111	536	1513	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 12:31:54,806] [INFO] DFAST Taxonomy check result was written to GCF_000337595.1_ASM33759v1_genomic.fna/tc_result.tsv
[2024-01-24 12:31:54,807] [INFO] ===== Taxonomy check completed =====
[2024-01-24 12:31:54,807] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 12:31:54,808] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4d93d2e2-438c-44ad-976c-2f1f6c508ead/dqc_reference/checkm_data
[2024-01-24 12:31:54,809] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 12:31:54,854] [INFO] Task started: CheckM
[2024-01-24 12:31:54,854] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000337595.1_ASM33759v1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000337595.1_ASM33759v1_genomic.fna/checkm_input GCF_000337595.1_ASM33759v1_genomic.fna/checkm_result
[2024-01-24 12:32:54,551] [INFO] Task succeeded: CheckM
[2024-01-24 12:32:54,553] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 8.33%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 12:32:54,574] [INFO] ===== Completeness check finished =====
[2024-01-24 12:32:54,574] [INFO] ===== Start GTDB Search =====
[2024-01-24 12:32:54,574] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000337595.1_ASM33759v1_genomic.fna/markers.fasta)
[2024-01-24 12:32:54,575] [INFO] Task started: Blastn
[2024-01-24 12:32:54,575] [INFO] Running command: blastn -query GCF_000337595.1_ASM33759v1_genomic.fna/markers.fasta -db /var/lib/cwl/stg4d93d2e2-438c-44ad-976c-2f1f6c508ead/dqc_reference/reference_markers_gtdb.fasta -out GCF_000337595.1_ASM33759v1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 12:32:55,050] [INFO] Task succeeded: Blastn
[2024-01-24 12:32:55,053] [INFO] Selected 7 target genomes.
[2024-01-24 12:32:55,053] [INFO] Target genome list was writen to GCF_000337595.1_ASM33759v1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 12:32:55,062] [INFO] Task started: fastANI
[2024-01-24 12:32:55,062] [INFO] Running command: fastANI --query /var/lib/cwl/stg4ff6d366-3dda-4453-89ad-19d461c590a7/GCF_000337595.1_ASM33759v1_genomic.fna.gz --refList GCF_000337595.1_ASM33759v1_genomic.fna/target_genomes_gtdb.txt --output GCF_000337595.1_ASM33759v1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 12:33:02,646] [INFO] Task succeeded: fastANI
[2024-01-24 12:33:02,653] [INFO] Found 7 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 12:33:02,653] [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_000337595.1	s__Natrialba taiwanensis	100.0	1509	1513	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.4145	N/A	N/A	N/A	N/A	1	conclusive
GCF_000337535.1	s__Natrialba aegyptia	95.4015	1293	1513	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.4145	N/A	N/A	N/A	N/A	1	-
GCF_000337555.1	s__Natrialba asiatica	93.9734	1188	1513	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_001861355.1	s__Natrialba sp001861355	82.0243	836	1513	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	81.7749	798	1513	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natrialba	95.0	N/A	N/A	N/A	N/A	1	-
GCF_008122205.1	s__Natronococcus sp008122205	80.1892	682	1513	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronococcus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_000230715.2	s__Natronobacterium gregoryi	79.4801	575	1513	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Natrialbaceae;g__Natronobacterium	95.0	99.99	99.97	1.00	1.00	4	-
--------------------------------------------------------------------------------
[2024-01-24 12:33:02,655] [INFO] GTDB search result was written to GCF_000337595.1_ASM33759v1_genomic.fna/result_gtdb.tsv
[2024-01-24 12:33:02,656] [INFO] ===== GTDB Search completed =====
[2024-01-24 12:33:02,659] [INFO] DFAST_QC result json was written to GCF_000337595.1_ASM33759v1_genomic.fna/dqc_result.json
[2024-01-24 12:33:02,659] [INFO] DFAST_QC completed!
[2024-01-24 12:33:02,659] [INFO] Total running time: 0h1m41s