[2024-01-24 13:17:34,680] [INFO] DFAST_QC pipeline started.
[2024-01-24 13:17:34,682] [INFO] DFAST_QC version: 0.5.7
[2024-01-24 13:17:34,682] [INFO] DQC Reference Directory: /var/lib/cwl/stg389ac8a6-1d12-4afb-9e97-ec28a688fdc4/dqc_reference
[2024-01-24 13:17:36,043] [INFO] ===== Start taxonomy check using ANI =====
[2024-01-24 13:17:36,044] [INFO] Task started: Prodigal
[2024-01-24 13:17:36,044] [INFO] Running command: gunzip -c /var/lib/cwl/stg9d0db0e3-0f88-4576-84d5-ff8d5e75f980/GCF_000283335.1_162.HSB1.1_genomic.fna.gz | prodigal -d GCF_000283335.1_162.HSB1.1_genomic.fna/cds.fna -a GCF_000283335.1_162.HSB1.1_genomic.fna/protein.faa -g 11 -q > /dev/null
[2024-01-24 13:18:00,659] [INFO] Task succeeded: Prodigal
[2024-01-24 13:18:00,660] [INFO] Task started: HMMsearch
[2024-01-24 13:18:00,660] [INFO] Running command: hmmsearch --tblout GCF_000283335.1_162.HSB1.1_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg389ac8a6-1d12-4afb-9e97-ec28a688fdc4/dqc_reference/reference_markers.hmm GCF_000283335.1_162.HSB1.1_genomic.fna/protein.faa > /dev/null
[2024-01-24 13:18:00,959] [INFO] Task succeeded: HMMsearch
[2024-01-24 13:18:00,962] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg9d0db0e3-0f88-4576-84d5-ff8d5e75f980/GCF_000283335.1_162.HSB1.1_genomic.fna.gz]
[2024-01-24 13:18:01,006] [INFO] Query marker FASTA was written to GCF_000283335.1_162.HSB1.1_genomic.fna/markers.fasta
[2024-01-24 13:18:01,007] [INFO] Task started: Blastn
[2024-01-24 13:18:01,007] [INFO] Running command: blastn -query GCF_000283335.1_162.HSB1.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg389ac8a6-1d12-4afb-9e97-ec28a688fdc4/dqc_reference/reference_markers.fasta -out GCF_000283335.1_162.HSB1.1_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:18:01,552] [INFO] Task succeeded: Blastn
[2024-01-24 13:18:01,555] [INFO] Selected 7 target genomes.
[2024-01-24 13:18:01,555] [INFO] Target genome list was writen to GCF_000283335.1_162.HSB1.1_genomic.fna/target_genomes.txt
[2024-01-24 13:18:01,560] [INFO] Task started: fastANI
[2024-01-24 13:18:01,560] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d0db0e3-0f88-4576-84d5-ff8d5e75f980/GCF_000283335.1_162.HSB1.1_genomic.fna.gz --refList GCF_000283335.1_162.HSB1.1_genomic.fna/target_genomes.txt --output GCF_000283335.1_162.HSB1.1_genomic.fna/fastani_result.tsv --threads 1
[2024-01-24 13:18:09,648] [INFO] Task succeeded: fastANI
[2024-01-24 13:18:09,649] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg389ac8a6-1d12-4afb-9e97-ec28a688fdc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2024-01-24 13:18:09,649] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg389ac8a6-1d12-4afb-9e97-ec28a688fdc4/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2024-01-24 13:18:09,657] [INFO] Found 7 fastANI hits (2 hits with ANI > threshold)
[2024-01-24 13:18:09,657] [INFO] The taxonomy check result is classified as 'inconclusive'.
[2024-01-24 13:18:09,657] [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
Halogranum salarium	strain=B-1	GCA_000283335.1	693851	693851	type	True	100.0	1488	1488	95	inconclusive
Halogranum rubrum	strain=CGMCC 1.7738	GCA_900114455.1	553466	553466	type	True	96.9201	1290	1488	95	inconclusive
Halogranum amylolyticum	strain=CGMCC 1.10121	GCA_900110465.1	660520	660520	type	True	84.5568	1030	1488	95	below_threshold
Halogranum gelatinilyticum	strain=CGMCC 1.10119	GCA_900103715.1	660521	660521	type	True	83.4107	871	1488	95	below_threshold
Haloprofundus halophilus	strain=NK23	GCA_003439925.1	2283527	2283527	type	True	79.8487	611	1488	95	below_threshold
Halogeometricum rufum	strain=CGMCC 1.7736	GCA_900112175.1	553469	553469	type	True	79.1277	615	1488	95	below_threshold
Haloferax litoreum	strain=MBLA0076	GCA_009674605.1	2666140	2666140	type	True	78.9915	531	1488	95	below_threshold
--------------------------------------------------------------------------------
[2024-01-24 13:18:09,659] [INFO] DFAST Taxonomy check result was written to GCF_000283335.1_162.HSB1.1_genomic.fna/tc_result.tsv
[2024-01-24 13:18:09,660] [INFO] ===== Taxonomy check completed =====
[2024-01-24 13:18:09,660] [INFO] ===== Start completeness check using CheckM =====
[2024-01-24 13:18:09,660] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg389ac8a6-1d12-4afb-9e97-ec28a688fdc4/dqc_reference/checkm_data
[2024-01-24 13:18:09,661] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2024-01-24 13:18:09,712] [INFO] Task started: CheckM
[2024-01-24 13:18:09,712] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCF_000283335.1_162.HSB1.1_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCF_000283335.1_162.HSB1.1_genomic.fna/checkm_input GCF_000283335.1_162.HSB1.1_genomic.fna/checkm_result
[2024-01-24 13:19:14,249] [INFO] Task succeeded: CheckM
[2024-01-24 13:19:14,250] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 95.83%
Contamintation: 4.17%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2024-01-24 13:19:14,271] [INFO] ===== Completeness check finished =====
[2024-01-24 13:19:14,272] [INFO] ===== Start GTDB Search =====
[2024-01-24 13:19:14,272] [INFO] Query marker FASTA already exists. Will reuse it. (GCF_000283335.1_162.HSB1.1_genomic.fna/markers.fasta)
[2024-01-24 13:19:14,273] [INFO] Task started: Blastn
[2024-01-24 13:19:14,273] [INFO] Running command: blastn -query GCF_000283335.1_162.HSB1.1_genomic.fna/markers.fasta -db /var/lib/cwl/stg389ac8a6-1d12-4afb-9e97-ec28a688fdc4/dqc_reference/reference_markers_gtdb.fasta -out GCF_000283335.1_162.HSB1.1_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2024-01-24 13:19:14,763] [INFO] Task succeeded: Blastn
[2024-01-24 13:19:14,767] [INFO] Selected 8 target genomes.
[2024-01-24 13:19:14,767] [INFO] Target genome list was writen to GCF_000283335.1_162.HSB1.1_genomic.fna/target_genomes_gtdb.txt
[2024-01-24 13:19:14,778] [INFO] Task started: fastANI
[2024-01-24 13:19:14,779] [INFO] Running command: fastANI --query /var/lib/cwl/stg9d0db0e3-0f88-4576-84d5-ff8d5e75f980/GCF_000283335.1_162.HSB1.1_genomic.fna.gz --refList GCF_000283335.1_162.HSB1.1_genomic.fna/target_genomes_gtdb.txt --output GCF_000283335.1_162.HSB1.1_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2024-01-24 13:19:22,752] [INFO] Task succeeded: fastANI
[2024-01-24 13:19:22,760] [INFO] Found 8 fastANI hits (1 hits with ANI > circumscription radius)
[2024-01-24 13:19:22,760] [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_900114455.1	s__Halogranum rubrum	96.9027	1291	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	97.00	97.00	0.87	0.87	2	conclusive
GCF_900110465.1	s__Halogranum amylolyticum	84.5527	1030	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900103715.1	s__Halogranum gelatinilyticum	83.406	870	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogranum	95.0	N/A	N/A	N/A	N/A	1	-
GCF_003439925.1	s__Haloprofundus halophilus	79.8154	615	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	98.76	98.76	0.93	0.93	2	-
GCF_001469955.1	s__Haloprofundus marisrubri	79.5968	629	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloprofundus	95.0	N/A	N/A	N/A	N/A	1	-
GCF_900112175.1	s__Halogeometricum rufum	79.1084	618	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	98.26	98.26	0.87	0.87	2	-
GCF_009674605.1	s__Haloferax sp009674605	79.013	529	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Haloferax	95.0	100.00	100.00	1.00	1.00	2	-
GCF_000337095.1	s__Halogeometricum pallidum	78.9146	609	1488	d__Archaea;p__Halobacteriota;c__Halobacteria;o__Halobacteriales;f__Haloferacaceae;g__Halogeometricum	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2024-01-24 13:19:22,765] [INFO] GTDB search result was written to GCF_000283335.1_162.HSB1.1_genomic.fna/result_gtdb.tsv
[2024-01-24 13:19:22,766] [INFO] ===== GTDB Search completed =====
[2024-01-24 13:19:22,773] [INFO] DFAST_QC result json was written to GCF_000283335.1_162.HSB1.1_genomic.fna/dqc_result.json
[2024-01-24 13:19:22,774] [INFO] DFAST_QC completed!
[2024-01-24 13:19:22,774] [INFO] Total running time: 0h1m48s